There are three marinas in San Juan [1], the largest being San Juan Bay Marina (787/721-8062), with a capacity of 191 boats, including 125 wet slips, 60 dry-stack spaces, and six spaces for yachts more than 100 feet long. There’s also a restaurant on-site.
Club Náutico de San Juan (787/722-0177) has 117 wet slips and Congrejas Yacht Club in Piñones [2] (787/791-1015) has 180 wet slips, a boat ramp, and a restaurant. All three have fuel and water.
Links:
[1] http://www.moon.com/destinations/puerto-rico/san-juan
[2] http://www.moon.com/destinations/puerto-rico/east-coast/loiza-and-pinones/sights/bosque-estatal-de-pinones