I'm confused by the first paragraph of your message.What do you have actual proof of, and what is the wrong trail?Maybe if you fill in as much of the following as you know for sure, we can help better:
1.DOB, DOM, DOD
2.You mentioned a will, when/where was it filed?Do you have a copy, and if so, does it mention any particulars on his family or origins?
3.Where exactly did he live in NY?
4.Do you have a physical copy of the death cert?Does it list the respondent/person supplying the info?If so, was it a child or a spouse?Is the spouse listed.
5.Do you have DOB, DOM, DOD on his son?And if you have death info, is mom listed?
6.Catholic or Protestant?Do you have any baptismal records?If so, are there any clues from either the god parents or mother's info?
7.If the son was listed as a minor without a guardian, check with the clerk of the county court as to whether there was ever a guardianship or emancipation hearing held.
Glad to help once the web gets untangled a little.Merry Christmas.