Have you checked out noonsite.com?
It would seem that NY is considered a port of entry.
Things being what they are these days I would call the NY Customs office listed on that page before you even enter US waters to make sure the 'proper protocols' are followed.
There have been some cruisers arrested in Australia for not following 'proper protocols'. I know the US is not OZ but the rule book got more complicated after 2001 and each office has a different chief paper pusher in charge who might take delight in ruining your day.
I hope it goes smoothly for you.