I think you all missed Jim Huber's topic; it wasn't where to go, it was how to get a rent a car!
Why on earth leave Manhattan by train or taxi or bus or whatever, simply to RENT A CAR?? Do you think that one of the largest cities on earth doesn't have adequate rent a cars in town?
Jim--plan and enjoy your time in Manhattan. Make a plan to rent a car IN MANHATTAN to take you away. I have done this several times myself. The only issue is juggling rate/location/brand of car rental (they change all the time).
Last time I was there to do this was about 1 year ago, last February school break. I spent 3 days in Manhattan with my daughter; had made a reservation for a Dollar car at their location at E 22nd Street. At the end our busy 3 days, we cabbed it down there; picked up a car and went. Because the car was from NYC, it could be returned to the airport at no drop charge. While that location on E 22nd seemed off the beaten path and was a $10 cab ride from 48th Street/8th Avenue where we were, it proved to be just a couple of blocks from an unfettered entrance to the FDR drive and we high-tailed it out of town to go to Massachusetts to visit my father. Nothing could have been more convenient. When we were done visiting Grandpa/Dad, we went right to LaGuardia and dropped the car there. Simple and easy. No trains involved.
You do not need to go throught the hassle and inconvenience of boarding a train to "get out of town" to get a rental car!
The only peculiar thing abour renting a car in the NYC area, airports included, does not affect you. That is, they don't rent to locals (better have your California driver's license handy) or if they do, the rate is about double or worse!