I would choose JFK because once you arrive, you don't have to change terminals -- in BOS you would have to get from Terminal E to Terminal B which requires taking a bus, walking through a parking garage, or a longer walk through Terminal C.

There will probably still be plenty of flights to CLT from both airports; I would actually consider the JFK schedule firmer because JFK has slot controls and BOS does not. If AA changes the schedule, you might be waiting longer for the next flight.