I left NYC via JFK about a month ago on the 9am flight. Security took about 2 minutes with Pre. I spent time in the Alaska Lounge which is really nice. The flight left on time as these are mostly west coast red eyes that are turning around so almost always arrive on time. My last flight was in a Boeing but it had the new satellite wifi and it was great and worked gate to gate. I don't know if you are in F or not but there have been a number of reports of the Airbus with the old interiors having broken F seats.

I have departed from EWR in the past. Security takes longer although its fine, the terminal is a dump, and you can use the Admirals Club if you are a Lounge member but its nothing fancy at all. EWR is also more prone to delays. I prefer JFK