Bit old of a thread, but in NY as long as you have catalytic converters and your tune doesn't stop the emissions tests from running you will be fine.
Pick up an OBDII code reader for like 50 bucks, and it should have a list of "readiness" checks. As long as those are running and say ready you'll do fine.
It was a pain in the ass on my old car because my normal setup had no CATs and a bigger turbo and injectors, and my tune would disable the checks so even if I had a CAT in it wouldn't work. Had to go to stock tune, injectors and put the CAT on and drive like a grandma because of the bigger turbo. This was a hyundai though, and the tuning solutions were shit and didnt let you control what it turned on and off.
