The shuttle is a route where it pays to be able to book in advance--if you can book your tickets 3+ weeks out, AA's prices tend to be quite reasonable but as you get closer in, they get a lot more expensive. JetBlue generally doesn't have these date-based cutoffs so if you need to book closer in, they'll probably be a lot cheaper.

Otherwise, AA is probably better. AA doesn't have the best operations, but JetBlue is even less reliable. As others have noticed, AA has more options when things go wrong. Their frequent flier program is better with good availability on this route (once again, you need to book several weeks in advance but if you do it's easy to get good value for award redemptions on this route).