As you probably know, it's illegal to use a scanner in your car in New York State, so your safest bet would probably be to put the scanner in the trunk with the antenna detached. That way, if you do encounter the police they probably won't see it, and even if they do look in your trunk for some reason, they can't possibly accuse you of using the scanner in the vehicle.
I give you this advice as an "average Joe". Perhaps someone else on this board with some experience in law enforcement can give you a more informed answer.