My friends and I were "stuck" in San Juan after our cruise since our flight didn't leave till 11pm that night and we had the BEST time- I am now dying to go back just to spend time in Puerto Rico!! We wandered around old San Juan starting from about 4:30 (all the historical buildings are open till 6pm, even on Sunday) and hit up the San Cristobal Fort (a UNESCO world heritage site, as is the other fort in old san juan- either one are not to be missed!) then got advice from the girl in the gift shop for a great little place for dinner. since it was the weekend there is basically a little craft fair set up along the waterfront in the evening with live professional salsa and marengue dancers, and we spent hours trying on beautiful jewelry made from "Sea glass" at one of the stalls, and my friend found the best Cappuchino she has ever had (and she is a coffee snob!).
old San Juan is amazingly beautiful with narrow streets cobbled in blue stone brought over as ballast on the treasure galleons from spain, and narrow houses painted in carribbean pastels. It was also much cleaner than many cities in the US and we felt very safe with plenty of people moving around in a very relaxed atmosphere.
I wouldn't bother with a sunset cruise for that day- enjoy the sights of Old San Juan, and you won't be disapointed!