When I went thru SJU a few months ago I cleared in Terminal A, rather than Terminal D as I always have in the past. I don't know if there's still an Immigration and Customs area in D, as D is all but empty. How busy it is depends on the time of day, and what flight(s) come in ahead of you. In the morning it has always been light. In the afternoon it gets busier.

There were a dozen or so kiosks, and either 1 or 2 Global Entry terminals. There were maybe 4 agents checking papers, and 1 assisting at the kiosks. I came in behind a JetBlue flight, so it took maybe 20 minutes to clear Immigration and Customs. You have to find one of the Agriculture baggage inspection checkpoints and get an APHIS sticker on your bags before checking bags or going to the TSA checkpoint.

I used the TSA checkpoint for Terminals B and C. There was a TSA Pre-Check lane on the left, and a 1st Class lane on the right, with everyone else in the middle. Like TSA checkpoints everywhere, how long it takes depends on how many agents are working, how many screening lines are open, and how many people are ahead of you. There's also a TSA checkpoint in Terminal A, but I have no experience with it. I don't think that Terminal D still has a TSA Checkpoint.