I did not notice any express check in facilities in NY when checking in for Legend on May 21. On the other hand, once inside the building ( that's another story), as long as the line seemed, the whole process took only 20 minutes.
Getting to the terminal was an adventure and it was being repeated on the 28th as we disembarked. It took some people hours to get the last quarter mile.
Whatever you do, do no approach the terminal by car, car service or taxi from the south bound West Side Highway. I would actually recommend not going near the pier with a car, taxi or car service. You will save hours by getting dropped off on the opposite side of the West side highway and walking across at one of the crosswalks with your luggage.