My thoughts on this matter are yet being formed and I have more questions than answers but I feel that there is very powerful evidence that William was indeed the father of our Gilbert of Carmel.

My thoughts are as follows:

1. The names: The very fact of the naming of the children is telling. This should not be readily discounted as the naming of children followed very common patterns in  those days with 1st born sons often being named after the father or grandfather (and 1st born daughters after the mother or grandmother). Later children were often named after Aunts and Uncles.  William having had a child named Cornby (Cornbury) is sufficiently odd to give one pause.  Cornbury was not a very common name, and moreover, it is a name which is recurrent only in our line of Merritt's. If William of Amenia did indeed have a wife named Tamer (Cornbury!?) who was the father of his son Gilbert and,  our Gilbert had a daughter named Tamer, this is yet again another naming coincidence that might not be so coincidental. I also believe that William was the first born son of our Gilbert Merritt  because he was the first male mentioned in the will.  Again it is interesting to note that this William had a son named Cornbury. 
The order of this Willam's children are as follows according to a Merritt Family Bible which came down through our line:
Gilbert Merritt 
Henry Merritt
Caleb Merritt (.m Hannah Eggleston lived at Vails Gate)
Cormbury Merritt
William Harison Merritt
Collman Merritt
Daniel Merritt
Hannah Merritt (m. Orin)
Lucie Merritt(Elizabeth) m. Whitney
Mary Merritt (m. Henry Brown)
Sarah Merritt
Deborah Merritt (m. Brotherton)

2.The Rye Connection: From what I can ascertain the mention of a Tamer married to a William Merritt actually comes from records in Rye NY, which supports the hypothesis that William was indeed from Rye and therefore the most likely candidate to be the son of Samuel as mentioned in the Rye records.

3. The Philipse Patent Plots

4. The Burials and records in Carmel

5. The Greene County move