Exploring San Juan is one option where you can:
1. go with the ship excursion
2. go with independent tour operators outside the ship
3. walk around on your own
4. take a 2 hour guided walking tour with email@example.com
I'd do (and am doing) the bioluminescence tour. From what I've seen this is an outstanding tour and not to be missed. I know I'll never get to see anything like this again so it's a "for sure" for us. You're lucky too that you have till midnight so you can pick from independent tours as well as your cruise ship. I've seen some great independents that I'd love to take but our ship leaves at 11 pm so I don't dare - it's cruise ship excursion for us.
Old San Juan at night is beautiful and romantic, however the forts will be closed. I loved walking around in the evening.
The kayak tour in bio bay is a cool thing to do, and can only be done at night. DO be SURE though to check the phase of the moon for that particular night. You can do so on several online weather web sites. The bioluminescence is best seen on a "moonless" night, which is accomlished by either the moon being a sliver or the sky being completely overcast. Also note that the tour will include rather a long bus trip from Old San Juan to the bay and back-it will be dark and not much to see out the window. Still it is a worthwhile thing to see.
I did check the moon phase and it looks great for July 18th which is when we're going to be there. I booked the excursion through Princess because of the tight timing at the end of the tour. They said the tour leaves at 4 pm.
Trying (endlessly) to get hold of the Legends of PR tour people to get out of the walking tour. We're booked from 2-4 and I can't end and begin all at the same time. Unfortunately the only other tour that day is 9-11 and we don't dock till 10 am. But of the two tours I really want the bio tour so that's the one we're going to stick with.