1st did you buy the vehicle in NY State and is it registered in NY State. If it was and registered as a new model it complies with all NY State regulations despite what the trooper mentioned otherwise it cannot have a Registration issued. If you bought the vehicle in New Jersey or Connecticut those same rules apply for tinting of windows, NJ is stricter than NY.. There are exceptions for the three states as far as emissions but that is not the matter before you.
In NY State has many of local courts especially town and village that are administered use magistrates that are non lawyers and most are part time., So take that in consideration when considering to contest this as they depending on the court can either be sympathetic or out right prickly, these individuals have great power with little knowledge.
If you decide to fight check out the local court personal and ask them what proof you need for your court date. And if decide to go to court, hope that the trooper is not there and citation will automatically be thrown out. If the officer does appear and does not give the proper information recited on the ticket as many just don't do there homework or even look at the ticket before them. This to will grounds for dismissal. Should you have the opportunity to cross exam the officer, be polite, but firm on the details. If a vehicle has not been alter and sold new in the last three states mentioned, would it not need to comply to all regulations before it could be registered. If they contend that it was altered, ask them how they know this, if they contend they use some instrument. As when was the last time the unit was calibrated, and then ask how often does the manual contend the unit needs to be calibrated. Also ask when the batteries were last changed in the unit. At this time also ask if they were wearing sunglasses or if they wear correction glasses at the time of the ticket. And then piece the two together. Also ask them the degree of tint and color they claim when was placed as a aftermarket, and if he is such an expert he could recite that as well . The one note of caution, should the judgement go against you depending on the which jurisdiction the court resides in, you could be liable for more than the ticket