Deacon Thomas Clarke was the son of James and Abigail (Lothrop) Clarke, born about 1658 based on his age at death, probably in Plymouth, (then) Plymouth Colony where his parents resided. His birth (and those of his siblings) was not recorded.
Thomas married three times. His first wife was Rebecca Miller, daughter of John and Margaret (Winslow) Miller of Yarmouth, Massachusetts, where they married on 15 February 1681. Rebecca died in Plymouth on 4 Apr 1688. His second wife was Elizabeth Crow whom he married in Plymouth on 12 February 1689. After Elizabeth's death in Plymouth on 13 Nov 1695,  he married Susanna Miller by 1700 probably in Plymouth, the younger sister of his first wife Rebecca. Susanna died in Plymouth in July 1721.
Thomas Clarke passed away in Plymouth on 20 March 1726 at age 68￼ and was buried in the White Horse Cemetery in Plymouth where his gravestone still stands:
The estate of "Deacon Thomas Clarke of Plymouth ... yeoman" was inventoried on 14 April 1727. In addition to the usual personal and household items was 60 ounces of silver valued at £45, and £119 in bills of public credit, £300 in debts due to the estate, £407 in the value of his homestead and houselot that "lyeth to the eastward of the way from Plymouth to Monument Ponds", in addition to several other lots of land in Plymouth and Middleboro. His inventory totaled nearly £1400, and his debts were less than £14. His son Thomas Clark was granted administration on his estate. The younger man's death occurred on 18 Mar 1728, and Josiah Morton of Plymouth was named as the successor administrator ("de bonis non") on the estate of his "father in law Deacon Thomas Clarke" on 27 July 1731.
In the settlement agreement dated 27 April 1727, son Thomas was to receive the homestead, and he to pay his sisters the sum of £352. Josiah Clark, son of the elder Thomas Clark, half of a 60 acre lot on Pine hills. The daughters were named as Susannah, wife of Elisha Holmes; Elizabeth, wife of Josiah Morton; Rebeckah Morton relict widow of Nathaniel Morton; Anna, wife of Gideon Ellis; Abigail, wife of Nathaniel Bartlett; and Sarah Clark (unmarried) daughter to Deacon Clark
1704 Sarah ye Daughter of Decon Clarke. ￼ Baptism
1709 Mary the wife of Thomas Clarke￼ This is confusing since all indications and past studies indicate he married in 1713. It could be a late entry in the wrong place. [Note: Mary was named as "Mary Clark" in her father's estate distribution in Feb. 1710, so the assumption is that she married before that date]
abt 1713 Thomas Clarke (son) marries Mary Ellis abt 1713￼ or earlier see 1709, but 1713 is less likely.
1713 Persons admitted -Thomas Clarke & Wife December 27, 1713
1714 Deacon Thomas Clarke’s son Thomas and wife Mary have their first child born, Mariah.￼
1717 (Son) Thomas Clarke 1717 Daughter Sarah Baptized￼
1727 Plymouth County Probate case 4400 Deacon Thomas Clarke’s Estate 27 April 1727 and Inventory 14 April, 1727. On 12 May 1727 Son of Deacon Thomas Clarke, Thomas, tasked to Administer.￼ 
1728 (Son) Thomas Clarke Chosen as deacon on 22 January 1728 but Thomas Clarke died on March 18th before ordination .
1728 Plymouth County Probate Case 4401: (Son) Thomas Clarke probate Administors are John Ellis of Sandwich, Ma. and Mary Clarke. Also mentioned Josiah Morton. ￼ John is most likely the son of Mordecae Ellis; Therefore, Mary is Modecae’s daughter and not the daughter of John Ellis of Medfield, also born in 1686. It is unclear to me whether this is the son or the father.
↑ 2.02.12.2 Find A Grave: Memorial #110891915, database and images (https://www.findagrave.com : accessed 10 January 2018), memorial page for Deacon Thomas Clarke (unknown–20 Mar 1726), Find A Grave Memorial no. 110891915, citing White Horse Cemetery, Plymouth, Plymouth County, Massachusetts, USA ; Maintained by Joan Ellis Pulis (contributor 47051328)
↑ William R. Librarian of the Woburn Public Library Cutter, "Miller, Cook, Clark, Hall, Crosby & Smith," NEHGR Vol. 51 (Jan. 1897), pp. 33-34.
"Thomas clark and Rebeckah Miller was mared the 15th of ffebuary 1681 in Yarmouth by Justes [Justice] Lathrop."
↑ Lee D. van Antwerp, compiler, Vital Records of Plymouth, Massachusetts to the Year 1850 (Camden, ME: Picton Press, 1993), p. 134.
"Rebkah, the wife of Thomas CLARKE, decd. 3d April 1688."
↑ Robert M. Sherman and Ruth Wilder Sherman, compilers, Vital Records of Yarmouth, MA to the year 1850 (Camden, ME: Picton Press, 1975, second printing 1993), p. 129.
"Rebekah Clarke daughter of the abovesaid John and Margreat Miller died upon the 4th day of April 1688."
↑ Lee D. van Antwerp, Vital Records of Plymouth, Massachusetts to the Year 1850 (Camden, ME: Picton Press, 1993), p. 86.
"Thomas CLARKE Sr. married Elizabeth CROW 12 Feb. 1689 or 90."
↑ "Massachusetts, Town Clerk, Vital and Town Records, 1626-2001," database with images, FamilySearch (https://familysearch.org/ark:/61903/1:1:Q29L-GZ74 : 3 November 2017), Thomas Sr. Clark and Elizabeth Crow, 12 Feb 1689; citing Marriage, Plymouth, Plymouth, Massachusetts, United States, , town clerk offices, Massachusetts; FHL microfilm 416,334.
↑ Lee D. van Antwerp, Vital Records of Plymouth, Massachusetts to the Year 1850 (Camden, ME: Picton Press, 1993), p. 135.
"Elizabeth, the wife of Deacon Thomas CLERKE, decd. 13th Nov. 1695."
I question if Thomas' second wife was the daughter of Yelverton Crow/ell. If she was, she would have been ten years older than her second husband. And if she was the widow Matthews, why does her marriage record call her "Crow" instead of Matthews? I think she's been misidentified, and further research on her parents is needed.
In the estate papers for Deacon Thomas Clark (file 4400), on 27 July 1731, Josiah Morton is assigned as administrator "de bonis non", meaning he became the second administrator after the death (or removal) of the first administrator, who had been the son Thomas Clark. Josiah was named admin. on the estate of his "father-in-law".
Possibly Find-A-Grave memorial 110891915 which would imply he has born around 1658. That would lessen the distance between Elizabeth Crowe/Crowell and himself at the time of marriage. Also his grandfather "was not" a Deacon. I'm still trying to sort that one out.