1 hour is a enough - just tight - if there's any kind of delay, it could be a problem. As long as you are traveling on 1 ticket, I wouldn't worry about it. If it's separate tickets, then it is riskier.

You do clear customs in San Juan - that's why global entry helps speed things up. Checked bags don't really make a difference - once we get to the bag claim in customs, they're usually waiting for us and you just drop them off right outside customs.