Newark is actually closer to Manhattan than either of the airports in the city, so anyone who plans to rent a car at the airport is better off flying into Newark and then driving through the Holland Tunnel (for downtown Manhattan or Brooklyn), Lincoln Tunnel (midtown) or GW Bridge (uptown). For your destination, the Holland would probably be the way to go.

If you're taking public transportation, though, LaGuardia is your best bet because you can get straight into the NYC public transit system, which is quicker and cheaper than the busses and trains from Newark into the city.

A bus from Newark Airport to Newark Penn Station (railroad depot) would allow you to enter the city by either of two different rail systems, NJTransit to Penn Station (34th St.) via the old Pennsy railroad, or another route that we used to call "the Tubes" or the "Hudson Tubes" whose new name I can't recall.

Avoid JFK if at all possible -- *unless* you can catch a super-cheap flight on JetBlue. Their fares are so low (and service is so good) that it's worth it to put up with the extra distance, traffic, etc., involved with patronizing New York's least convenient airport. Only problem with JetBlue is that they serve only a few cities outside NYC, and provide only one or two flights a day in each direction per city. Check out jetblue.com, or click this link to their website's page showing routes and cities:

http://www.jetblue.com/travelinfo/routemap.html