We've done the ferry twice. No major issues. Sitting having a drink while waiting for the ferry was nice. Waiting in all the long lines at customs at both ends was not. One trip the ferry was blasting gospel music (I think it was a sunday morning). I had not problem with the music, would have been nice, had it not been at an ear piercing volume..
I much prefer relaxing for an hour or two at San Juan, grabbing a bite to eat and then enjoying the great views on our flight.
We are fortunate coming from Boston though as we have a lot of options in timing with JetBlue.
Having read most of the topics on this over time, it seems pretty clear that there's no "best" option - What's best really depends on where someone is coming from.
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