Always prefer EWR personally.

Never had any queues at Immigration and getting into central Manhattan by train is just so easy with that monorail transfer to the mainline and then 20-25 minutes or so into New York (Penn) station. All for about $10 each way IIRC.

But just remember to get off at New York (Penn), not Newark (Penn). The latter is a bit grim...and is not in Manhattan at all. Apparently this confuses lots of innocent tourists where English is not their first language - particularly as even "Newark" and "New York" are also close in spelling and even pronunciation.

Newark (Penn) is NOT a good place to finish up in late at night