Have never been to JFK so can't really say but the where I come from it is advised to try to avoid that airport, just like you really need to avoid Heathrow. There are just some airports with to much trouble.
Depending on your choices and funds you can select your route to be the most convenient and through easy airports.
I have good (and smooth) experienc e.g. with Atlanta International.
Since we usually fly the other way around, I always try to make the pond-jump on the first leg of the trip (while going 'on' vacation) because local flights are much more frequent then intercontinental flight. At least then you know your luggage is on the same side of the Atlantic as you are and you will probably be re-united with it the same day.
When going home.... I don't really care as I'm going back to a filled closet.