It sounds like you may be familiar with the requirements of FOPA:
https://en.m.wikipedia.org/wiki/Firearm_Owners_Protection_Act
https://www.law.cornell.edu/uscode/text/18/926A
This is an affirmative defense, so you may have to make this defense in court, which will really slow your trip.
There's no duty to inform in either state, so if you are pulled over I recommend saying nothing unless asked.
But you won't be pulled over, because you will drive the speed limit. And you will fill up on gas and snacks just outside of those states (I recognize Boston to Buffalo is a long way, just stick to rest plazas if you must stop)
I can't speak to the likelyhood of the cops ignoring FOPA. The only case in MA I'm aware of, the gun wasn't properly stored. The farther away from NYC you are, the better you'll be. Some upstate NY cops are actually pro-gun!
I recommend getting into PA as soon as you can, even if it adds an hour, it's already a multi hour drive.
The magazines over 10 rounds are an unknown. FOPA was passed before any laws against magazines. I think it's probably covered, but if it's only a few PMags, why not ditch them? Buy a few in PA, keep them for the trip, and mail them back home before you return to NY/MA.
There's another option that would help for MA. For $200 and a trip to Chelsea, MA you can get a non-resident LTC, which provides lifetime protection against criminal charges for firearm and ammunition possession. NY, as far as I know, makes it impossible to legally possess a pistol for non-residents. Non-assaulty rifles and shotguns and ammunition therefor in NY are probably the thing you have to worry about the least.