If you stay at any of the Marriott hotels near the Newark Airport (free parking) they all provide free shuttle service to the airport tram system which will take you to the train station - the train takes you into Manhattan to Penn Station 32nd street (under Madison Square Garden) - it takes about an hour each way - depending upon how you hit your connections - a cab ride is around $90 plus tip each way. You can also stay at the Marriot Brooklyn Bridge - parking will cost you about $18/day and a cab to mid-town will run about $20. You can also take the subway ($2). Or if the weather is nice walk to Manhattan over the Brooklyn Bridge - the view is magnificent!
The Stamford, CT Marriott is right across from the train station. MetroNorth to Grand Central Terminal is $37 round trip off-peak. The trains run at least every hour all day and night. Less than an hour trip into the city. If you stay at either the Courtyard or Fairfield Inn near JFK they offer shuttles to the Jamaica train station (LIRR) or the Howard Avenue subway station. The Brooklyn Bridge Marriott is a nice hotel in a very nice section of Brooklyn. There are subway stops nearby. Parking there is very reasonable compared to most places in the city.
The Courtyard in Jersey City is next door to the PATH train, which is $3.50 RT into several stations in NYC.,,and it's quick.. Just MHO but if you stay at the airport, you'll spend lots more time getting in and out of the city than I would want to spend..:0 The train from CT costs more and also takes up more time Gotta factor in transportation costs