This has NOTHING to do with FOPA. FOPA only applies when travelling through a state, with the gun unloaded & locked and with ammo locked in a separate case, all in the luggage area, and you don't stop for anything other than gas (even potty breaks are not allowed). FOPA (as relevant here) refers only to continuous passage thru a state.
What NY is cracking down on is people who are not just passing through. If one's destination is in NY, or one is changing modes of transport in NY (ex.: drive in, get on plane, fly out), FOPA does not apply under these conditions.