Join Date: Aug 2010
Location: LGA - JFK
Programs: UA, AA, DL, B6, CX, KE, Latitude, VIFP, Crown & Anchor, etc.
Posts: 2,589
OP, clarity on your questions & see if we understood - to best help you.
You are flying into EWR/JFK for a cruise, plan to stay 3 days post-cruise? If so, where do you plan to stay in NYC/Manhattan or NJ side as you mention going to PHL also so it sound liked post-cruise? Then, your plan is to checkout & drive the car to JFK to dropoff, and catch your flight home?
Parking is very expensive in Manhatttan - $40 to $50 overnight near/below most hotel's or nearby underground garage. Staying in Manhattan, use mass transit - we don't drive into the Manhattan, just PITA and $$.
If you pickup your rental deal in EWR and drive into Manhattan - it's at much as $15 cash toll one-way only, ouch . Going to JFK, it can be toll-less if you know your way around & allow enough travel time due to unpredictable traffic, better than LAX and you know how I-5 and I-10 and I-405 can be like at all hours.
If you are driving the rental pre-cruise for 3 days, then it's different and post-cruise, going straight to JFK - best advice I can give, as above, take a flat-rate taxi. Or, depending on departure time - taxi to NY Penn Station - LIRR train to JFKAirTrain or taxi to subway train to JFK AirTrain (don't confuse it with NJ Transit to EWR AirTrain as someone else recently claimed.)
We are leaving this Sunday out of MCT (on NCL's Breakaway) for a week toward warmer weather. Please checkout Cruisecritic forum as we have plenty of FAQ, insider's tip and East Coast Departure/NYC Board have plenty of details for you. Logistics for cruise transport are a bit more complicated.