I am quite sure you mean two daily flights you can take to get to where you are going (you don't say where that is), because I'm almost positive that Delta has more then two flights a day out of both airports.

You may want to consider dropping the car off as soon as you get into Manhattan if you are staying there a few days. If you are staying in the city all you will do is pay to park it someplace, it's totally useless in the city. Then take the bus out to the airport you choose, and not deal with returning it at the airports at all.

Given the choice, Newark is easier to return a car to then JFK is until they get the airtrain running there.