Since you don't have any error reports, and GSX is working too, the problem doesn't have anything to do with JFK.
The most common cause of crash at the airport, is an AI traffic model which is not fully compatible with P3D (or has a missing/corrupted texture), so you are mislead thinking the cause it's the airport, because it only happens when you go there, but that's just because that particular model appears at JFK, because of its livery and schedule and yes, non-compatible and/or missing/corrupted AI textures are known to cause the sim to crash.
The easiest way to verify this, is try the scenery with all the AI Traffic sliders set to Zero.