AA seems to be ceding market share - and destinations served - in the NYC market rather than growing.
Delta's JFK facilities are a pit in the truest sense and that would likely be enough to keep me from making them my primary carrier in the region, assuming you'd be taking flights that are only served from JFK versus their other operations.
I really like the jetBlue product and their FF program,
True Blue 2, is coming around though it still doesn't have quite the same potential upside as the legacy programs. it will be interesting to see what happens in the next few months with them as they try to integrate Lufthansa and Aer Lingus more into their scheme.
And there is CO over at EWR. I generally like their product, too, though not as much in-flight as B6.
Depending on where you are headed for your trips you'll have vastly different experiences.