One advantage of arriving at EWR is the short Airtrain ride to the airport from which you can purchase a transfer from the cruise line that will take you from the airport to the cruise port. And I'm quite sure that a transfer by the cruise line is a guaranteed connection. Taxis, city buses and Uber are not guaranteed and if something goes wrong there's some chance your ship may sail without you. And no cruise line I've used will sell transfers to or from a train station.
In addition, while I've never been to either Penn Station,, the airport, or Liberty Cruise Port, if you intend on getting there with time to spare that spare time would be best spent in the best environment with the best waiting areas, food, drink and restrooms. I'm guessing the airport would be the best. Trip Advisor probably has reviews and photos of all three of those places.
The most important thing is to insure as best you can that you do indeed get on the cruise ship. What you decide to do after getting off the cruise ship after the cruise is a secondary concern.
DW and I almost always go by train to a cruise port and never plan on arriving the day of the cruise. We ALWAYS get there the day before and spend the night in a hotel. ALWAYS!