(Byram is an unincorporated village in Greenwich, CT.  It remains a mystery, to me, why our subject is called, "Thomas of Rye" because the Town of Rye is in New York State, across the Byram River from Greenwich, CT.)

1.  Clarence Almon Torrey.  1997.  New England Marriages Prior to 1700.  Genealogical Publ. Co., Baltimore, MD.  On p. 481:

LYON, Thomas & 1/wf Joanna WINTHROP (1630-); ca 1647, 1649?; Fairfield

LYON, Thomas & 2/wf Mary HOYT, m/2 John WILSON...; ca 1654; Stamford, CT

Dates are birthyears of earliest known child as an indicator of approximate year of marriage.  Locations are known residences of the husband.

2.  Robert B. Miller & Albert Brown Lyons, eds.  1907. Lyon Memorial III:  New York Families Descended from the Immigrant Thomas Lyon of Rye.  Self-published. [W. Graham Printing Co., Detroit, MI.]  539 pp.  (facsimile reprint available from Higginson Books; online at Ancestry.com, where images are not entirely readable):

p. 20	THOMAS LYON OF RYE THOMAS LYON "of Rye" was born in England§ about 1621, and died at Byram Neck, Greenwich, Fairfield Co., Conn. in 1690.  He was buried in the old Lyon family burying ground at Byram Neck.  He is supposed to have come first to the Massachusetts Colony, and thence to have gone to seek his fortune in the far west of Fairfield County, Conn., where at about the same time Richard and Henry Lyon, presumably his brothers or cousins,† appeared.  His first wife was Marth Joanna Winthrop, a grand-daughter of Gov. John Winthrop, of Salem, Mass., and it is to Hon. Robert C. Winthrop, a lineal descendant of the Governor that we are indebted for nearly all the circumstantial knowledge we have of the life of Thomas Lyon... §The statement which has been often repeated that Thomas Lyon was from Yorkshire, England, appears to have no foundation... †Thomas Lyon was in Stamford as early as 1647; Henry Lyon in Milford 1649, Fairfield 1652, later in Newark, N.J.; Richard Lyon in Fairfield in 1649.  That the families of Thomas and Richard were intimately related is shown by the fact that Abigail, daughter of Thomas Lyon married John Banks, Jr., while Elizabeth, daughter of Richard Lyon, married Benjamin a brother of John Banks Jr.
	While Y-DNA testing has proven that Richard and Henry LYON are closely related, it has also proven that neither is remotely related to our subject, Thomas LYON of Rye.
p. 42	Thomas Lyon married for his second wife, about 1654, Mary Hoyt, daughter of Simon Hoyt, of Stamford, Conn., by whom he had four sons and four daughters.
p. 45	Children of Thomas and Martha Johanna (Winthrop) Lyon:   2.   I.   _____; d. in infancy.   3.   II.   Mary [Marie]; b. Aug. 1649; d. before 1713; m. John Willson. Children of Thomas and Mary (Hoyt) Lyon:   4.   III.   Abigail; b. about 1654-5; d. before 1713; m. John Banks.   5.   IV.   John; d. 1735?; m._____   6.   V.   Thomas; d. 1739; m. Abigail Ogden.   7.   VI.   Samuel; d. about 1713; unm.   8.   VII.   Joseph; b. 1677; d. Feb. 21, 1761; m. Sarah _____.   9.   VIII.   Elizabeth; d. before Nov. 1713; m. John Marshall.   10.   IX.   Deborah; m. _____ Cone.   11.   X.   Sarah; m. _____ Merritt. ...

.  Lyon(s) Families Association of America: Database (on CD as of 22 Feb 2010; these are member submissions).

.  David Dobson.  1985.  Directory of Scottish Settlers in North America, 1625-1825.  Vol. 5.  Genealogical Publ. Co., Baltimore, MD (Broderbund CD-354).  On p. 145:

Primary Individual: Lyon, Thomas; Place: America; Year: 1649. Date of emigration and intended destination or place and date of first mention of residence in the New World.  A majority of the data is (sic) on those who settled in Canada.

.  Donald A. Whyte.  1986.  A Dictionary of Scottish Emigrants to the USA. Vol. 2.  Magna Carta Book Co., Baltimore, MD (Broderbund CD-354).  On p. 80:

Primary Individual: Lyon, Thomas; Place: Connecticut; Year: 1621-1648.

.  "English & Welsh Emigrant Index." The English Genealogist 4(2): 368-372 (Broderbund CD-354).  On p. 370:

Primary Individual: Lyon, Thomas; Place: Connecticut.

.  Meredith B. Colket, Jr.  1975.  Founders of Early American Families: Emigrants from Europe, 1607-1657.  General Court of the Order of Founders and Patriots of America, Cleveland, OH (Broderbund CD-354).  On p. 185:

Primary Individual: Lyon, Thomas; Place: Connecticut; Year: 1647.

.  Colonial America, 1607-1789 CT Census Index (online at GenealogyLibrary.com):

Lyon, Thomas

CT

Fairfield Co.

Fairfield

1671

.  From the "Book Notices" of the July, 1909, issue of the The New England Historical and Genealogical Register, vol. 63, p. 303, reviewing:  Robert B. Miller & A.B. Lyons, eds.  1907. New York Famililes descended from the immigrant Thomas Lyon of Rye, with introductory chapter by Dr. G.W.A. Lyon on the English Lyon families.  William Graham Printing Co., Detroit, MI.

This third volume of the Lyon Memorials deals with the descendants of Thomas, who settled in Fairfield County, Conn.  These descendants soon removed to New York.  One of the most praiseworthy features of the volume is the index of places which covers all three books of the series and will be very helpful in finding any particular ancestor.  Supplements to volume one, which treats of the families of William of Roxbury and of Peter and George of Dorchester, and to volume two, which deals with the descendants of two brothers who went to Fairfield, Conn., are also included in this book in addition to the records of more than thirteen hundred descendants in these New York families.

.  Descendants of Simon Hoyt.

.  Schneiderman, Faline.  Nov 2014 - Jan 2016.  Documentary Study: Byram Cemetery and Lyon Cemetery, Greenwich, CT.  Historical Perspectives, Inc. (hpi@historicalperspectives.org) Westport, CT, for the Conservation Commission, Town of Greenwich, CT  (PDF file online at www.greenwichct.org):

p. i	In August, 2014, it came to the attention of the Town of Greenwich, Connecticut, that there was an encroachment on a parcel of land historically known as the Byram and/or Lyon Cemetery... in Greenwich...
p. ii	The historical record is very clear that the Lyon and Banks families held slaves during the years that they lived on Byrum Neck, and for the Banks family, this included both African-American and Native-American peoples.  It is quite likely that a burial plot was established for thie population, which was not an uncommon practice.  Thomas Lyon, being a Quaker, and his immediate descendants, may have believed that it was a just and fair thing to do — to provide their slaves with a specific burying ground.  Later generations would have likely followed suit.
	This paragraph is inconsistant in that it first makes it appear only the BANKS family had slaves, then implies the LYON family had them, too.
p. 2	Located along Long Island Sount at what is now the border between Connecticut and New York, Byram is an unincorporated village in the Town of Greenwich...

.  Message Nos. 146, 148, 152 in the Lyon Family Genealogy Forum (online at GenForum.com).

.  Chris Lester's  Lester Family Genealogy web site [link died], citing Lyon Memorial volume.

.  Family TreeMaker.  World Family Trees.  Vol. 38, Pedigree No. 115.

.  Encyclopedia Britannica CD 98.

.  GEDCOM provided by descendant.