You are allowed to carry anywhere in NYS but the 5 boroughs of NYC. no problem in Nassau or Suffolk counties. As far as travelling through the city, you may not stop your journey for any reason other than for gasoline. No food, nothing. While travelling through the boroughs, the gun MUST be unloaded, cased and locked with ammo separately cased and locked.
I know this because as a NYC permit holder and expert I have much experience with this. The problem that we have all read and heard about regarding people getting arrested and in big time trouble is because they were caught or voluntarily admitted possessing guns in NYC, the city being their destination, not while travelling through it. Show me one example where someone was arrested travelling through NYC from a locale where they were licensed to carry to another where they were licensed to carry and were arrested. I guarantee you are legal if you follow my directions.
There is no need whatsoever to call and notify anyone nor get permission from anyone. While I am sick and tired of all the BS that the city makes law abiding citizens go through, and the way visitors are treated when carrying in error, the laws are not confusing. Maybe convoluted, but not confusing... It is very simple. NYC doesn't recognize CCW from anywhere or anyone that is not LEO or a NYC CCW. Again, while I disagree with the ways of NYC in this matter am I am sick and tired of people making bull$&@( up about how the city operates. It is asinine yes, but straightforward. SORRY.
Anyway, regarding the OP, as long as he follows my directions whic fall under FOPA he will be fine. My final word is this... Even if he follows the letter of the law as I have outlined, that doesn't mean some JO cop who doesn't know the law won't arrrest him if the possession should somehow come to light. How that would be I do not know. i.e. Don't speed through or have a kilo of coke in the trunk. But the problem of LEOs who are ignorant of the law can happen anywhere not just NYC, as we have all seen and read about in numerous cases regarding open carry etc...