Ok, my answer is going to be different than those above.

Since you are leaving on Delta, I would first check to see which airport has more flights going to your destination. My guess would be JFK. I have been stuck at EWR because Delta cancelled a flight for whatever reason and have been out of luck. In inclement weather, more flights do leave JFK than EWR as well.

It may be more of an inconvenience to return a rental car to JFK, but the greater # of flights to your destination (if that is the case) and the more likely flights will leave JFK over EWR may make the extra cost worth it.