Never allow leo to search your trunk-ever!!!
But if your license is good (not suspended, revoked) and you don't intend to break any laws while in NYC, why would you have to worry whether it's legal? If you were stopped for a traffic infraction (speeding, running a stop sign, etc) the police can't search your trunk if you don't give them permission, and they would have no reason to get a warrant, so it shouldn't be an issue. Just arguing from the standpoint of reason here. Even if you did get pulled over and the cops did search your trunk, it would be an illegal search and seizure and would have to be thrown out of court.
The key is to NEVER EVER EVER give the police authority to search your trunk. EVER!!! Even if they try to scare you by claiming that they will get a warrant and if they find anything you will be in big trouble, just laugh and say "go ahead and get your warrant". The truth is that most search and seizures are either done illegally or because the driver gave permission, thinking that cooperating will be in their best interest. As soon as you give the cops permission to search your trunk, you have given up your best defense, the protection against illegal search and seizure. Even if they were to illegally search your trunk (after you said NO to allowing them to search your trunk, of course!) and they found something, you will still get arrested just like you would if you were to grant permission, and you would still go to jail, but at least the law is on your side in that the item(s) found were illegally obtained and therefore inadmissible in court, so the charges would have to be dropped eventually.
Another reason to NEVER allow the police to search your trunk is that even if, in YOUR opinion, you don't have anything to hide and think it will cause the police to let you go sooner if you were to cooperate, they could find something completely legal that they decide to consider a "weapon" or "burglary tools" such as a baseball bat or crow bar or screw driver or the like, and charge you. Probably wouldn't have happened if you had just said NO from the get go. So remember kids, JUST SAY NO TO DRUGS AND LEO!!
And for you LEO's who will want to chime in and say that this type of thing never happens, I will just say right now, GIVE ME A BREAK!