I don't know what it is like going through SJU since the storms, but we have gone through in the past and made it from de-planing to gate in an hour. We have always given ourselves 2-3 hours and had lunch/dinner between flights. We've also always used Cape Air to get to SJU from EIS and they've always been reliable. We often would get to EIS early and they'd get us on an earlier flight as well.

We have global entry, so we breeze through customs, but I've usually felt it hasn't saved us a whole lot of time since it has typically been quite. Our trips have varied throughout various times of the year as well, although the majority have been May-Oct.