Don't take a taxi into Manhatten from either airport...unless
I fly in and out of both more times a year than I want to, so here are my pointers:
1. From/to EWR by taxi means crossing a state border and means fares double. Take the train into Penn Station and you are away, the service is pretty good.
2. Taxi down the Van Wyck is horrendous most times a day, and along with the shuttle horrendous. It is usually quicker but more tiring to get the Air Train to Jamaica and LIRR into Penn Station.
3. Unless you have time the subway to JFK on A/C lines can prove long and frustrating. But Cheap.
4. New Jersey Transit to Penn Station is frequent, quick and inexpensive.
5. Where you are staying in Manhatten can make a serious impact on your decision.
6. If time of departure is important for JFK, probably not for EWR, then an airport hotel is very good value for money.
7. At JFK the BA lounges are pure crap, except for Long Island Chardonneys in the BA Business class lounge. The First Class lounge is a bad joke by BA on its clientele.
8. The EWR lounge is better, but only opens 3 hours in advance of flights when CX check in opens whereas JFK is not.
9. EWR security is quite efficient in the evening and compares to Fast Track at JFK if you can check in at the Business Class counter.
10. If you have an APEC card then JFK is better for arrival.
Safe travelling!