The Marriott at the airport is very nice..Easy to get the train to the city from the airport train's link..

Another vote for the EWR Marriott. It's on airport property and a stone's throw from the terminals. we stay there whenever we have an early flight out of EWR. As the previous poster said - it's also easy to get the train from the city or you have two other options: a) You can rent a car (most major rental companies have on-airport locations and drive into the city or b) you can taxi a taxi.

When you check out for your flight you can take their free shuttle to the terminal or if you are feeling energetic you can walk across the main parking lot to the closest terminal (if it's not the one that services your airline simply take the air tram between terminals to the one you need.

If the Marriott doesn't appeal to you, just about every major hotel chain has a place "off airport property" but within a mile or two of the airport - most have free shuttle service. You can find a list of hotels here:
http://newark.airporthotelguide.com/airporthotels.html

I've stayed at several hotels around EWR and also at the Marriott. (Was just there the night before last.) The others tend to be in complete no-man's-land locations, while the Marriott is right there. Good food, good bed, good night.

And since the Marriott is right at the airport, you will have the easiest, least expensive method to reach Manhattan.

Thanks, everyone. Sounds like the Marriott is the hands-down winner!