A check of the 1810 census of Boston shows no white male Thomas FISHER with a wife (only an unmarried non-European of that name), so a birth in England seems likely, unless Thomas arrived after the census with a pregnant wife or was simply not head-of-household.  With names this common, it's going to be very difficult to prove where our subject was born and who, exactly, were his parents.  Y-DNA testing could be very valuable in "crossing the pond" to at least connect with his FISHER origin.

— born Rancho del Laguna Seca, Alta California [later known as Coyote, now part of San Jose, Santa Clara Co., CA]:
5.  Maria Liberata Eulogia FISHER, b. 1846-48; bap. 23 Apr 1848, Mission San Jose, Santa Clara Co., CA 
6.  Fiacro Cornelio FISHER, b. 1850

1a.  Email from Rondi Frankel (28 May 2009):

There is a baptismal record for Maria Liberata Eulogia, daughter - possibly illegitimate - of Liberata Ceseña and William Sturgis Hinckley, at Mission San Jose, on 23 April 1848. The record number is 10827, found at the Huntington Library site mission records.

1b.  Email from Jeanne Rudy (6 Mar 2010):

Re:  Maria Liberata Eulogia Fisher:    I have seen the microfilm of the baptismal record, too (I accessed it at Santa Clara University Archives).  It is difficult to read, as are many microfilmed records ... the HINCKLEY confusion stems from a penciled notation made in the left-hand margin by someone trying to transcribe the surnames on the old records.  If you look closely at the baptismal description, you can see that her father is "Guillermo Ficher".  "Ficher" is a very common misspelling for Fisher, esp. in old Spanish records. Eulogia, as well as her younger brother, Fiacro (my gr-grandfather), were natural-born children of William Fisher and Liberata Cesena.

2.  1850 Census Every-Name-Index/Images (online at Ancestry.com):  the Santa Clara County Census was lost.

3.  1860 Census Every-Name-Index/Images (online at Ancestry.com, Image #3 of 5 — indexed "Puattii"):  San José P.O., Burnett Twp., Santa Clara Co., CA, Roll M653_65, p. 257, PN 35, 291/25, enumerated 13 Jun 1860, official enumeration date 1 Jun 1860 (extracted by Diana Gale Matthiesen):

Liberata Peiattii?	40	F					Mexico
Thomas      "	19	M		day laborer			Cal
Cyprian     "	17	M		"    "			"
William     "	15	M		"    "			"
Oliva       "	13	F					"
Theaco?     "	10	M					"
George      "	7	M					"
Pedro       "	2	M					"
Carlo Evolas	22	M					Mexico

Thomas [Tomas], Cyprian [Cypriano / Cipriano], William [Guillermo], Oliva [Eulogia], and Theaco [Fiacro] are Liberata's children with her first husband, Capt. William J. FISHER.  George is Liberata's son with  Dr. George H. BULL.  Pedro must be Primitivo, Liberata's son with Caesar PIATTI.  Carlo EVOLAS appears to be hired help.

4.  1870 Census Every-Name-Index/Images (online at Ancestry.com, Image #127 of 318):  Alviso P.O., City of San Jose (Ward 1), Santa Clara Co., CA, Roll M593_88, p. 243, PN 39, enumerated 21 Jul 1870, official enumeration date 1 Jun 1870 (extracted by Diana Gale Matthiesen):

1870:  for an explanation of the column headings, please see What the Numbers in the Federal Census Mean (missing columns contained no data).

1

2

3

4

5

6

7

8

9

10

11

12

15

19

316

310

Piatti Cesar

43

M

W

Grocer ret.

20,000

5,000

Italy

/

/

/

______ Liberata

50

F

W

Keeping house

Mexico

/

/

______ George

16

M

W

California

/

/

/

______ Primitivo

12

M

W

"

/

/

/

Ah Trunk

45

M

C

Domestic Servt.

China

/

/

__ Mary

30

F

C

"       "

"

Fisher Amelia

8

F

W

California

Caesar PIATTI is Liberata's third husband.  George is Liberata's son by her second husband, George H. BULL.  Primitivo is Liberata's son by Caesar PIATTI.  Amelia FISHER is Liberata's granddaughter.

5.  1880 Census Every-Name-Index/Images (online at Ancestry.com, Image #30 of 48):  507 6th St., San Jose, Santa Clara Co., CA, Roll T9_81, p. 100B, PN 30, SD 1, ED 246, enumerated 14 Jun 1880, official enumeration date 1 Jun 1880 (extracted by Diana Gale Matthiesen):

1880:  for an explanation of the column headings, please see What the Numbers in the Federal Census Mean (missing columns contained no data).

1

2

3

4

5

6

8

9

10

11

13

23

24

25

26

*

507

239

243

Piatti Liberata

W

F

60

/

Farmer

/

Lower California

L Cal

L Cal

______ Primitivo

W

M

21

Son

/

Works on Stock farm

California

Mass

L Cal

Rota Eulogia

W

F

32

Dau

/

At Home

California

Mass

L Cal

Fisher Amelia

W

F

18

GDau

/

At Home

California

L Cal

L Cal

*6th St

6.  1890 Census:  the 1890 Census Population Schedules were destroyed.

6.  1900 Census Every-Name-Index/Images (online at Ancestry.com, Image #16 of 40 — indexed "Nannette Beattie"):  334 Sixth Street, San Jose (Ward 3), San Jose Twp., Santa Clara Co., CA, Roll T623_111, p. 87B, SN 8, SD 2, Ed 69, enumerated 7 Jun 1900, official enumeration date 1 Jun 1900 (extracted by Diana Gale Matthiesen):

1900:  for an explanation of the column headings, please see What the Numbers in the Federal Census Mean (missing columns contained no data).

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

19

20

21

22

23

24

25

26

27

*

334

154

177

Fisher Amelia

Head

W

F

Jan 1863

37

S

CA

Mex

Mex

Book Keeper

0

Y

Y

Y

O

F

H

Beattie Navaretta

GMother

W

F

Mar 1818

82

M

65

1

1

Mex

Mex

Mex

Y

Y

N

Rota Eulora

Mother

W

F

Mar 1849

52

M

10

1

1

CA

Mex

Mex

Y

Y

Y

Fisher Fred

Bro

W

M

Nov 1880

19

S

Mex

"

"

Laborer

4

Y

Y

Y

Fisher Annette

Sister

W

M

Feb 1890

10

S

Mex

"

"

At school

10

Y

Y

Y

*Sixth Street

"Navaretta Beattie" is a misspelling of Liberata PIATTI.  Eulogia (FISHER) ROTA was childless, so she cannot be Amelia's mother; if Amelia is Liberata's granddaughter, then Eulogia would be her aunt.  Eulogia's father was born in either England or Massachusetts, not Mexico.

8.  Anon.  5 Dec 1905.  Obituary.  San Jose Mercury, San Jose, CA (as submitted to the Somos Primos web site by Jeanne Rudy):

Mother of Mrs. Murphy-Columbet Passes Peacefully Away. Mrs. Liberata C. Piatti died yesterday morning at 10 O'clock at her home, 314 South Sixth Street.  She was the mother of Mrs. Murphy-Columbet, Thomas Fisher, C. Fisher (of Mexico), Mrs. E. Rota (San Jose), Fiacro Fisher (S.J.), George Bull (San Jose) and P. Piatti (Salinas). Her death was caused by a severe attack of pneumonia which disease had her in its grip but 2 days and from which she could not escape, owing to her advanced age which was 87 years, 10 months, 28 days.  She was probably the oldest pioneer in California and was known from one end of the state to the other. Mrs. Piatti was born in Cape San Lucas, Lower California, where she met and married her first husband, William Fisher, who had come in his own vessel around the horn in 1843 to California where he landed at Monterey.  He went into Lower California exploring the country and later met his bride.  With her he came to Monterey in May 1846 on the ship Maria Teresa.  Mr. Fisher died in 1850 and several years later she married George Bull.  Again misfortune met her when Mr. Bull died in 1854.  In the course of time she met and married Mr. Piatti, a native of Milan, Italy.  With her first husband she laid out the great Laguna Seca Rancho on which she resided until the death of Mr. Piatti in 1899.  The funeral will be held at St. Joseph's Church tomorrow morning at 9:30 o'clock.  All the children will be present except C. Fisher who is now in Mexico.  A solemn requiem mass will be sung for the repose of her soul. Interment will take place at Santa Clara.

9.  Pablo L. Martínez.  1965.  "Guía Familiar de Baja California" [Vital Statiscs of Lower California].  Cited in a post on the FISHER Surname Board (online at Ancestry.com); here paraphrased and condensed by DGM:

William FISHER, immigrant from America, was baptized in San José del Cabo on 29 May 1830 as José Guillermo CESEÑA, after Cipriano CESEÑA, father of his future wife, Liberata CESEÑA.  William & Liberata had five (sic) children:  María, Fiacro, twins Thomas/Tomás and Cipriano (b. 1 Nov 1842), and William/Guillermo.  William & Liberata are said to have moved to Alta California after 1844.  Some of the children later returned to Baja.

10.  Anon. [Preface by J.P. Munro-Fraser].  1881. History of Santa Clara County, California.  Alley, Bowen & Co., San Francisco, CA (online at HeritageQuest at Genealogy.com). On p. 571:

Captain William Fisher (Deceased).  This old pioneer was born in Boston, Massachusetts, in the year 1813.  At the age of twelve years he left home and shipped on board a vessel for three years, hoping to benefit his health which had been delicate.  At the end of three years he returned to his native State, but soon after sailed for Upper California.  Not long after he proceeded to Lower California where he built a small vessel, and in company with Captain Hanks, made the trip to Mazatlan, on which voyage she was wrecked.  He lived for many years in Lower California, and about 1845 came to this county and bought the Ranch Laguna Seca, comprising four square leagues.  He then brought his family up to this valley, where they arrived in the month of April, 1846.  He now stocked his property with horses and cattle, at the same time conducting a mercantile business in San José, the latter of which he disposed of, on account of ill health, in 1849, to Josiah Belden, who was his clerk at the time, and retired to his ranch to manage its affairs.  He was not one of those who went to the mines at the time of that great excitement.  Captain Fisher in all his intercourse with the emigrant proved himself an invaluable friend, while his name is indelibly connected with the early history of San José in which chapter his name will be found linked with many a good and noteworthy action.  He died April 5, 1850.  Married, in 1834, Señorita Liberata Cesaña, a native of Lower California by who he had a family consisting of Mary C., now Mrs. D. Murphy; Thomas M.; Cyprino William (deceased); Uloga Frico.

The lack of punctuation makes it appear there are just four children when, as we know, there are six; that is, Cyprino William is Cypriano and William while Uloga Frico is Eulogia and Friaco.

11.  Eugene T. Sawyer.  1922.  History of Santa Clara County, California.  Historic Record Co., Los Angeles, CA (online at HeritageQuest at Genealogy.com).

p. 721

FIACRO JULIAN FISHER.—The Fisher family have been identified with the Santa Clara Valley since early pioneer days...  The father, Fiacro C. Fisher, was born upon the farm in Burnett township, Santa Clara County, August 30, 1850, the youngest son of William and Liberata (Cesena) Fisher, early settlers of California.  The paternal grandfather was of English birth and a seafaring man by occupation.  He came to the United States in young manhood, and in 1830 left his first locaiton in Massachusetts for California, making the voyage as mate of a vessel.  He located at San Jose [del Cabo], in Lower California, and owned a vessel which he navigated upon the Gulf of California.  In April, 1842, he came to this state and bought the ranch known then as the Laguna Seca Grant, and four years later brought his family to Monterey.  Upon this property he engaged in cattle and stockraising until his death, which occurred in 1850, at the age of forty years.  The maternal grandmother, Liberata Cesena, was a native of Mexico and survived her husband many years.  They were the parents of four sons and two daughters: Thomas N. and Cypriano, twins; William, deceased; Fiacro, Mary, the wife of Murphy Columet (sic), and Eulogia...

Mary FISHER was not the wife of "Murphy COLUMET," she married first Dan MURPHY and second Peter J. COLUMBET.

12.  Robert G. Fisher (of San Jose, CA).  nd.  Rancho del Refugio de la Laguna Seca and the Captain William Fisher Family (submitted by Jeanne Rudy and online at the Somos Primos web site; copies said to be deposited at all Santa Clara County libraries).  Excellent compilation and certainly the best currently on the web.

13.  Natural Diversity of Motorcycle County Park (online at the County of Santa Clara, California, web site [link died]).  Due to copyright restrictions, I have had to paraphrase the following extraction (see web site for full account): 

Much of the Motercycle County Park — on the Coyote River in southeastern Santa Clara County, California — consists of land that was once part of a roughly 20,000 acre land grant called Rancho Laguna Seca, awarded to  Juan ALVIREZ in 1834 by Governor FIGUEROA, when the State of California was still Alta California, México.  In April of 1842, Rancho Laguna Seca was purchased at public auction by William FISHER for $6000. William FISHER was born in England in 1810.  He immigrated to Massachusetts as a young man and sailed to Baja California in 1830.  He settled in San Jose del Cabo, where he owned a boat and plied the Gulf of California.  In Mexico, William FISHER married Liberata CESENA; they had four sons and two daughters.  Four years after purchasing Rancho Laguna Seca, William erected an adobe home on the current site of Coyote Ranch, now part of Santa Clara County's Coyote Creek Parkway, where William engaged in stock ranching until his death in 1850.

It is unclear whether William was born in England or in New England (i.e., in Boston, MA).

14.  Email from the staff at Santa Clara Mission Cemetery.

15.  Messages posted to the FISHER Surname Board (online at Ancestry.com).

16.  Email from Roberto J. Martinez Fisher (8/05).