There is particular uncertainty about adoption agencies, as this New York Sun article makes clear:

As the question of same-gender marriage in New York goes down to the wire at Albany, experts on the legal impact of the changes being sought are warning that religious exemptions in Governor Cuomo’s bill have fallen far short of what the religious community had been praying for.

Professor Wilson’s letter is significant not only because of her distinction in the field but because the issues she is raising are the point at which a number of senators are on tenterhooks. Ms. Wilson is one of six law professors or experts who signed a May 17 letter to the majority leader of the Senate, Dean Skelos, warning that “conflicts between same-sex marriage and religious conscience will be both certain and considerable if adequate protections are not provided.”

... [Their] warning comes as both Mr. Cuomo and Mayor Bloomberg have been orchestrating what the Archbishop of New York, Timothy Dolan, has called a stampede to get the legislation passed this session. The religious community has for several years been seeking a formal hearing at which these issues could be addressed, but it was curtly spurned in the Assembly by the speaker, Sheldon Silver, in 2007, and no hearings have been held in either chamber since then.