Each state has its own laws regarding sales tax applicability, so you need to check with the revenue department or DMV in your home state. Most states have reciprocity agreements under which sales tax paid in one state offsets tax you would owe in your home state when you register the vehicle there for the first time. Of course, if NY sales tax rate is greater than CT sales tax rate, you will be charged the difference as a use tax when you register your vehicle in NY. All of this assumes that you intend to register the vehicle in NY and not in CT.