score:5
Newark airport is well set-up for car rentals, so seems to be the obvious drop-off point, however the public transport connections do have a few annoyances.
The airtrain (monorail) will take you to Newark Liberty Station, but charges a hefty $5.50 to exit - airtrain is free inside the airport, but that little connection to the amtrak lines is annoyingly expensive.
Trains from Liberty do go to Newark Penn Station and thence all the way into Manhattan , or you can switch the PATH at Newark Penn Station. The real annoyance about this though is timing of the service: only two trains an hour, which is bad enough, but they are at 32 mins past the hour, and 42 minutes past the hour. So you can quite easily have 45 minute wait for a train.
An alternative is the local bus $2.75 to Newark Penn Station, plus all the shuttle buses to Manhatten.
My suggestion: avoid the airport, drop the car at one of the rental places at Newark Penn Station and take the PATH.
Upvote:4
Newark Liberty Airport.
From there you can catch either the bus or the train (Airtrain to Newark Liberty, then on to NY Penn) into Manhattan.