I've done both, and I actually prefer ATL. But, given the above choices I would go through Charlotte. Of course, this depends on the airline you are flying. American will fly through CLT, and this is typically okay ... especially when compared to Philadelphia which can be a borderline disaster. I would not book anything, however, with less than a 2 hour layover. Especially coming back. JFK can be fine if you go with JetBlue and possibly Delta. Got stranded at JFK once with Delta when they didn't have enough pilots for our connecting flight home that night. Wife and I slept in those hard airport chairs that night. Once again, give yourself extra time on the layover when you return because you'll likely need it if customs is backed-up. I would suggest a 2-1/2 to 3 hour layover coming back. Been there and done that. Hope this helps.