I know this is an old post, but I was wondering the same thing as I'll be travelling from MA to PA to shoot with my old man. I read that the NY courts didn't interpret FOPA to apply to airport travel (even diversions!), but I couldn't find an example of somebody getting arrested while following FOPA protocol in a car. Still being cautious, I decided to ask the State Police if they had a non-resident permit for transport, knowing the answer was going to be "no" and hoping they would cite FOPA. This is the response I got via email, doesn't mean a LEO in the southern part of the state won't decide to do things his own way, but I'll feel better having this printed and I'll leave my pre-bans at home.
"There is no non-resident pistol permit for the purpose of transporting firearms through New York State. You will be covered under the Federal provisions of 18 USC § 926A which states that the firearm must be unloaded, in a case, and stored in the trunk of the vehicle. If your vehicle has no trunk, it must be unloaded in a locked case inaccessible to the driver and passengers. A locked case does not include the glove-box or console. Necessary stops for gas or rest stops are permissible. This covers you for a continuous, uninterrupted travel through NYS. Also note, 18 USC § 926A - Interstate transportation of firearms, does not apply to magazines. In NYS, you can not possess a magazine with a capacity of greater than 10 rounds.
If you have any further questions, please re-contact me.
Inv. C.A. Hunt, NYSP-Pistol Permit Bureau"