I'm going to list this as an answer although you will want to corroborate. Genealogical Dictionary of Maine & NH on page 710 (Waldron entry) asserts that Major Richard's brother George had a son William but says nothing further of him (that I saw anyway). George's profile right now is orphaned and poorly sourced so I'd start there.
Now here's a problem: one of the "Deceit" sources (In the Devil's Snare) says that William was the son of Richard, not his nephew but cites no sources. I couldn't find "Trouble to the Eastward" and the Documentary History of Maine Vol 6 does mention William Waldron several times but did not specify his relationship to Richard.
Marriage of George Waldron & Bridget Rice appears in parish register 31 May 1635 at Alcester, her name transcribed as "Rie".<ref>"England Marriages, 1538–1973", database, FamilySearch (https://familysearch.org/ark:/61903/1:1:NVYS-B8Z : 13 March 2020), George Walderne, 1635.</ref>
And William baptized at Alcester 4 August 1639 as son of George & Bridget.<ref>"England Births and Christenings, 1538-1975", database, FamilySearch (https://familysearch.org/ark:/61903/1:1:JMFL-VL8 : 19 September 2020), William Walderne, 1639.</ref> I'd say this is your guy.
I would also note that NEHGR 9:56 in it's article on early settlers of Dover, NH says that the William who was taxed in Dover in 1664 was born in 1642, was called "nephew of Maj. Waldron" (i.e. Richard) and says "it would seem must be son to William" (i.e. the brother of Richard who drowned in 1646). This may be possible but I would look for Dover tax records to see how this William was described and where his supposed birth of 1642 comes from since we now know that Richard's brother George had a son William born 1639 and George also lived in Dover. The only mention made of George in this article is that he was taxed at Cocheco in 1672 as George "Wallden" so the author was apparently unaware of George's wife Bridget and his multiple children including a William.