Hahahaha, JFK better than EWR? Seriously? I've only had once or twice at EWR having to spend more than an hour waiting to take off. Whereas, JFK is around the 95% mark. Oh, add to the fact that JFK is a dump that has no PC.
As stated earlier, all airlines with major NYC operations have lots of elites on all flights. I would absolutely stick with CO. (Have you ever been inside of Delta's T2?)
I can understand the EQM argument, but in no way would that force me to the arms of another airline.