You will always be better off with all your flights on one ticket. So Jet Blue with a connecting Cape Air flight has advantages. Or American out of Miami.
We’re on the plane about to take off for San Juan, so I will have latest information in a few hours. I’m expecting midweek will not be bad, because so much depends on when you are traveling, among other factors.
I would not be comfortable with checked bags and 80 minutes connection time on two different tickets.
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