We have transited through SJU twice in the past 2 months. In both cases, we were on single tickets with JetBlue. We have global entry, but it did not help either time as there was essentially no line at customs & immigration. As mentioned, we were forced out of the secured area, and required to clear security again. TSA pre was helpful in getting back through security quickly.

A word of caution regarding the tight connections however.......both of our Silver codeshare flights were extremely late departing EIS. An hour might be enough time to make the connection if everything goes smoothly. That said, there have been far too many travel issues lately for me to feel comfortable with that tight a connection. Understanding the desire not to have to return the boat super early, I would still opt for the earlier EIS departure to afford you more time in SJU. Just my humble opinion.