JFK experience is way better (including refurbished CW Check-in and separate premium security arrangements). Haven't been to EWR in ages, but the JFK lounges also have the Elemis Spa (which EWR does not) and decent showers.
Don't know how the pre-flight dining experience compare, but JFK has a buffett arrangement with a fairly wide choice.
JFK is very much BA's best and most premium service outside of LHR.
JFK has the added benefit of mostly 744 service