The major delay I've encountered when disembarking in NYC is the huge taxi line, or mob, once you get outside the terminal. Our first time, we waited 45 minutes for a taxi. Now, we walk across the street, head toward 11th Avenue, and usually find a taxi within minutes.
For Penn Station, I wouldn't book anything before 2:00-2:30, assuming disembarkation begins at noon. Those with flights or cruise line transfers are usually let off first. You can also opt to carry off all of your own bags -- in other words, check nothing -- and you will be among the first passengers off the ship. (Which could still be crowded if many have the same idea.)