Although there is the Safe Passage Act it is practically ignored in those states. If you are stopped in those states and they find a firearm they will find a way to arrest you and let the judge figure out the rest.
This is untrue. ALL of the widely-publicized arrests in NY and NJ in the past few years have involved people who were NOT covered by the FOPA, with the exception of Gregg Revell, the man who was arrested at Newark Airport after spending a night in an
airport hotel due to a missed connection. And the problem there is that the drafters of the FOPA weren't thinking about air travel (or bus or train travel) when they wrote the law -- this was in 1968 and the safe travel provision was an afterthought, and all they were thinking about was individuals transporting their guns in their own private cars. Gregg Revell should have been covered, but due to the automobile-specific language of the FOPA you can see why/how an anti-gun agency like the NY/NJ Port Authority could twist it to claim he wasn't covered.
The nursing student who was arrested in NYC? Not covered by FOPA because her possession of the gun in NYC wasn't legal. The Tea Party lawyer from CA who was arrested at the airport when leaving NY to return to CA? Also not covered, because he had spent several days in NYC
illegally possessing a handgun.
Let's face it -- New York state is a complete barrier between the states west of NY and all of the New England states. If you want to visit New England, you somehow have to traverse NY state. My brother is in CT and my sister is in NH. I have carry permits from both states. I transport up the NJ Turnpike in strict accord with the FOPA (with one exception-- see below), and I skirt around NYC into CT. I haven't been stopped so the waters have not been tested, but I don't think I would be arrested if stopped.
FWIW, NJ state law echoes the FOPA language almost exactly, so if you are traveling through NJ by car I doubt there would be any problem, especially on the Turnpike, which is patrolled by the State Police. The language of the NJ version is right on the NJSP web site. The
caveat is that NJ changed one important word: Where the FOPA says the firearm "OR" the ammunition must be in a locked container, NJ says "AND." So I transport any firearms in their own locked cases, and I put ammo in an old Craftsman mechanic's tool box and padlock the hasp. (I drive an SUV, so I don't have a separate trunk.)