Straycat...so you booked a hotel room, dropped off your luggage, then toured NYC?
I prefer to stay in Manhattan for a few days then fly out of LaGuardia.
I refuse to travel on any bus or train with all the luggage from a cruise. Did that once when I disembarked at the NYC port and took the Long Island Railroad to my mother's house. Not a pretty sight getting down escalators and on the railroad with luggage. The only good thing was that it was Saturday, because those LIRR commuters would have killed me getting on with luggage. I know, because I used to commute.
I have enough trouble slepping my luggage out of the port terminal let alone getting on a bus or train.
I still think Bayonne needs to have some kind of Shuttle to NYC from the port. The cruiselines should set something up.