Been through EWR dozens of times and a few through JFK and LGA too. The train is nice to avoid traffic but a bit of a walk/airtrain from the terminals. If you're comfortable with trains and public transit in genearl, that would be my recommendation to at least get to the city (same as Canada101 said).
Otherwise, it's awfully nice to have the UberXL pull up and you just relax until drop off at your hotel.
Those are my options depending on where I'm arriving from, time of day, and who is with me.
There is also a bus that runs to the heart of NYC but that one takes a little more courage. The train has interesting people. The bus has
really interesting people.
