Definitely fly into EWR. If you are concerned about Murphy's Law, fly in the day before, because if your 7am flight gets cancelled, you're probably screwed getting to Newark to board the ship.
If you fly in the day before, here are some options of places to stay:
Residence Inn by Marriott Newark, Extended Stay America Suites Elizabeth, Embassy Suites by Hilton Newark Airport, and/or Hampton Inn and Suites Newark Airport Elizabeth. They are all in the same relative area. They probably all have free transport from the airport, and you can check about transport to the port, or call an Uber/Lyft.