We have been to San Juan many times, and still like it. I suggest that you get off and take a taxi up to El Morro. The fort will be closed, but you can still see the outside of it, and gaze down onto the cemetary. Then you can wander your way back down to the piers. Just keep to the beaten path, as in any city, and you will be fine. You could also just take a taxi back down to the piers, but then you would miss the flavor of OSJ.
Last time, when we got off the ship, we went to our left and took an excursion on a Segway. It was really fun! This is an option of something to do, also.
There is a
night tour of OSJ that is recommended over on CC.
Here is a link to
Frommer's walking tour.
Here is a
map of OSJ, with links to different places.
We enjoyed dinner at El Jibarito on Calle Sol.
Don't miss OSJ. It is a neat place to visit.