I wish I could have good news for you. You are not the first to be arrested by the NY Port Authority. New York does not recognize Title 18 an exemption--they recognize it only as a defense. Their pistol possession laws are presumptive felonies. You will have to get a lawyer. If you belong to the NRA, call them for help.
In regards to firearm offenses, you must hire a lawyer who is a firearms law expert. Ask to examine his record regarding firearms cases.
Democracy is two wolves and a lamb voting on what to have for lunch. Liberty is a well-armed lamb contesting the vote. NRA CSSA GOA 2AF CCRKBA / Tactical Pistol Instructor