Is New York your destination, or *a* destination as part of whatever trip you are making? The problem that I see most boaters would have is while they may be cruising to somewhere else, they may be spending a few days in the state which puts the provisions of FOPA (federal law which is supposed to protect your right to transport from a jurisdiction where you have a right to possess the firearm, to another jurisdiction where you you have right to possess the firearm) as poor protection under the circumstances considering New York law, not to mention county or city ordinances.
The only opinion which matters is that of the law enforcement officer who contacts you (unlikely, though a safety check or boarding in NY may involve questions about firearms? No idea.) and the District Attorney. The law in NY broadly stated is that you may not possess a handgun without permit and registration, and there is no reciprocity, and no way to obtain one for mere mortals who are not residents. FOPA is often disregarded, or interpreted strictly (direct route, no stopping etc.) I would not want to be in the position of arguing my boat is my home even if it was my home and that isn’t really a defense to NY law anyhow.
There is another federal statute commonly known as LEOSA which allows active and retired law enforcement officers from anywhere in the US to carry (with some restrictions) in every state/locality - which is supposed to preempt state and local laws on the subject. Regardless, LEOs are regularly hassled and even charged in NY and NJ, and subjected to additional requirements that were supposed to be preempted.