Hi Kris... If you stick around Isla Verde (the name of the main tourist beach in San Juan) its super safe. All the nice hotel chains are lined up there. Nice big beach, plenty of space for launching/landing. There is a kite school there (
http://www.15knots.com) and those guys are really cool. If you bring a couple kites and need a size to match conditions you can always rent from them (Cabrinha). There are a few economy hotels / motels there too... just do a google search for hotels on/near isla verde, San Juan. Its right next to the SJU airport. Some good night life right near the kite school too. I would classify the water quality at Isla Verde medium chop on a 13-17 day. (Think of Deer Creek, but not quite as bad and no boat wakes). 12m is the most popular kite to use as trade winds are typically anywhere from 13-18 kts out of ENE (side-on). You need to launch on the beach then body drag through the buoy/ swimming area before you can water start (about 75 meters).
There are some other really cool flat water spots that are isolated... One is called Playa Las Picuas in the Rio Grande Section. Smaller beach... requires some advanced self launch/land skills. let me know if you need more details and I can send you a map pin of the exact spot. Its a little sketchier in terms of safety (meaning people), but Ive never had any issues. The safety of the kite conditions are super good... always a side-on wind. The Westin Rio Mar is right next to it. My avatar picture is from this flat water spot.
My condo is I Palmas Del Mar on a crescent moon shaped beach (about an hour south of San Juan on South East Coast). Very tricky launch and strong current toward shore so tough to stay upwind for longer than an hour session, but the swells are big (6-8 feet) Super fun too boost off them and ride some in. They of course get smaller toward the beach break but fun to ride. Requires a beach landing and walk back up to the point to take off again if you decide to ride some waves in. Otherwise you can stay upwind and boost off the swells.
let me know if you need more details and I can fill you in. I love kiting here.... You can do a pretty good budget trip if you stick around Isla Verde for 4 or 5 days. If you have a 12m or 14m with good depower range, you can kite pretty much every day on just one kite and then rent from the kite shop if you need smaller.