I asked a similar question on the runnerworld forum last month before I left for vacation in San Juan, and I got response, which I am unable to pull up now.  They've been having some issues with their forums, I'm not sure where the old post went.  Anyway, I didn't get the response until after I got home, so I wasn't able to follow his advice, but apparently there is a nice running path near the convention center in San Juan, downtown.  Where are you staying?  I stayed in Isla Verde for a few nights and ran on the beach there, which I would reccomend if you enjoy beach running.  Once I got downtown to San Juan I just used the hotel treadmill, because without knowing a predestined path, the city is not very runner friendly.  If I can pull up the response to my post with the details of the convention center path, I'll let you know.