If the MyHeritage smartmatches are to be believed, then Ephraim Judson is his father. I don't want to merge them yet until I can find further proof.
I got excited because I found something here about Daniel's father, except that's the wrong generation because Elisha's trip took place in 1825. Elisha is his son, not his father.
'''''History of Fulton County, 1892''''', page 157
Frothingham, Washington, b. 1822
https://archive.org/details/historyoffultonc00frot/page/n8
In that same pdf on page 73 of the Family Sketches section (page 789/902 of the pdf) There's a paragraph about the Judson family beginning at Daniel.
Daniel moved to New York from Connecticut in 1740 at the age of 11. He surely came with his parents but I can find no mention of them. They helped settle the area so they probably died before there was a a church to keep records or maintain a cemetery. Finding their records in Connecticut will be tricky without knowing the parent's names. This history was written after 1921 nearly 200 after his birth.
http://www.schenectadyhistory.org/resources/mvgw/bios/judson_john.html
First elected Deacon in Kingsborough, NY in 1793 and re-elected deacon of the United Church in 1804.
The church history says "The first settlement of Kingsborough was in the year 1786", so Daniel couldn't have moved to Kingsborough when he was 10. If that sentence about him moving there at age 10 is wrong that makes it more likely that he could have married Lois in Milford, CT.
But I guess that sentence could have just meant that he moved somewhere in the Mohawk Valley then. It had white settlements when he was 10. Lois's brother Elisha Clark died in Milton, about 30 miles away so maybe that's where Daniel lived before he moved to Kingborough.
1793-1876. Kingsboro, N.Y. Presbyterian Church: Historical! Delivered ...
By George Harkness
https://books.google.com/books?id=FZVAAAAAYAAJ&pg=PA10&dq=d...
Here's something I found in a search result in google books. However, the actual book is unavailable. Saratoga Co. is close to Kingsborough. Milton is around 80 miles away, on the Hudson River.
"Marvin H. Vann, HC 60-4920, Fort Valley, VA 22652 (150) LEWIS / CLARK - Seek par. and w. of William LEWIS, b. at Farmington, Conn.(?), ca. ... 1813; and Parthena, b. 1751, d. 1848. The latter m. Elisha CLARK and they settled in Saratoga Co., N.Y."