I've been spending some time over at werelate.org (a Genealogy wiki), volunteering for a "Match & Merge" project and as a result have spent many intense hours this last week trying to understand the early Wheelers of New England.
The challenge of distinguishing them all seems immense to me.Especially the early Thomases:
1. The "senior" as you call him, son of Thomas by his first wife back in Cranfield, who initially settled in Concord until 1644 when he and others left for CT.
2. The younger brother, son of Cranfield Thomas by his second wife Rebecca, who was likely Capt. Thomas Wheeler of King Philip's War, wounded there (along with his son by the same name, both of whom died probably of their wounds by the end of 1676).
3. Thomas, son of #1 above who may or may not have gone to Connecticut with his father.
4. One you don't mention, but who I came across frequently was Thomas of Boston, married to Rebecca, who died 16:3:54 in Boston (NEHGR 10:218) and whose will was proved 25 July 1654? (NEHGR 5:305). He had a daughter named Rebecca who married John Curtis 26 Dec 1661 (NEHGR 20:43).
How do you know that Thomas #2 ever left Concord and went to Connecticut, much less went into Westchester? (Although I love your theory, I'm just trying to distinguish all those Thomases...)
Related: which one was he who was called Sargt in 1642 in Concord and married to Sarah Miriam with a child Timothy (b. 1667), and who died in 1704? (NEHGR 87:56) [Is this #3 above?]
Who was the Thomas Wheeler who died in 1686, mentioned in Thomas Starr's will (NEHGR 95:132)
Who was the Thomas Wheeler who was constable in Concord in 1671? (NEHGR 112:122) #3 above?
There apaprently was also a Thomas Wheeler in Lynn, MA 1649-1653 (NEHGR 8:166)
Who was the Thomas Wheeler who owed a debt to the estate of Comfort Starr in 1659 in Boston (NEHGR 9:224)?
As you can see, I'm still working on all of this, but your query about the Captain and supposed links to Westchester really caught my attention.