I have used both and that depends upon:
- Cost of flight
- Where my first stop is in the New York conurbation
- How much time I want to spend at the airport - which is an unknown, as you do not know how bad it's going to be. Although, the last time I left from JFK from push-back to rotation was 50 minutes of taxi/wait, taxi/wait.
- Time of day for arrival and departure
As mentioned, the EWR monorail (free) is good and the train to Penn is easy. From JFK the cheapest is the coach (last year it was $14 I think) and works well, dropping you by Grand Central. It picks up at every terminal.
So, there is no simple answer.