From what I've been told you can't even pass through NY with a handgun in your car unless you have it registered there...or something like that. I know when I use to live in NJ and we would head out to a range in PA we would have to travel around this one NY town (even though it was quicker to go through) because of it. Again, that is what I was told by a guy I was with that was like deathly afraid of it, but I couldn't find the law and didn't want to find out the hard way.
http://www.handgunlaw.us/
The best way to travel through NY or any state that has restrict ion is to carry a copy of Title 19Part 1
Chapter 44 926A pf the federal code with you. Some law enforcement may not know the law. DO
keep the firearm in a locked box. Keep ammo in another locked box. No ammo in Magazines or speed
loaders. In the t runk or if no trunk as far back in the vehicle as possible in a locked box. This covers all
bases. All of this may not be necessary but it may save you some gr ief.