The Bayonne port is actually New Jersey, not New York, but it is very close to NY. Here is an article regarding the problem. We parked here for a week on our recent Explorer cruise and did not have any damage to our vehicle.
The spray paint problem had been reported more often a year or so ago, but it was my understanding that the parking area was moved from the painting, so problems were gone. There was a recent complaint however, so perhaps this is becoming a problem once again.
Article here:
Royal Caribbean passengers beware: vehicles being damaged permanently at Port Liberty Cruise Terminal : Jackson NJ Regional Opinions News Reviews – Jackson Howell Freehold Lakewood Toms River