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I don't believe there are any storage lockers, but I know that there used to be a place as of a couple of years ago where you could pay to store luggage in the airport. I believe it was near the American check in counters.

If for some reason it is no longer there, a strategy that I have often used (not in San Juan, but elsewhere), is that I will take my luggage into a larger, nice hotel and take it over to the bellman and ask to store it, just like I was a hotel guest who needed to stare luggage for a few hours. That works almost every time. There is a hotel connected to the airport and you could try to do that there if there's no longer a storage facility in the airport or, worse case, take your bag with you to Old San Juan and do it there (although there aren't many large hotels there).

Of course, the most obvious thing would be to see if you could just go ahead and check it in with the next airline you will be taking later that day, if you are flying on from SJU that day. Most airlines will take luggage at least 6 hours in advance.