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  Sir John Bernard Burke.  1939.  Genealogical and Heraldic History of the Landed Gentry.  16th ed.  Burke's Peerage, London (reprinted 1996 as Burke's American Families with British Ancestry.  Genealogical Publ. Co., Baltimore, MD).  On p. 2572 (boldface added):

CHARLES ANDERSON BOSTON, of New York City, b. 30 Aug. 1863; m. Ethel Gustava, dau. of Edward Lyon, of New York City, a descendant of Richard Lyon, of Perthshire, Member of Cromwell's Army, who emigrated to America in 1648, son of John Lyon, of Auldbar, and grandson of Sir Thomas Lyon, styled Master of Glamis (d. 1608) and his wife, Eupheme, dau. of the 7th Earl of Morton.  Sir Thomas Lyon was the son of John Lyon, 7th Lord Glamis (see BURKE'S Peerage, STRATHMORE, E.).

On the assumption that our subject is Richard's brother, then this is Thomas's ancestry, too; however, there is no proof of the connection, and most sources show no issue for Sir John LYON and Euphemia GLEDSTANES. 

3.  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.

4.  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.

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

Primary Individual: Lyon, Thomas; Place: Connecticut.

6.  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.

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

Lyon, Richard	CT	Fairfield Co.	Fairfield	1671
Lyon, Thomas	CT	Fairfield Co.	Fairfield	1671

8.  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.

9.  Descendants of Simon Hoyt.

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

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

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

13.  Encyclopedia Britannica CD 98.