Just came back from 5 days in Isla Verde/San Juan. Like recommended here, we avoided the hotels and ate in and around San Juan. To be honest with you, we didn't have the best of luck with the local places. Here's a list of where we ate, ranked from top to bottom:
Pikayo (in the Puerto Rican museum of art in Santurce) - not authentic local cuisine, but uses local cuisine/flavors as inspiration. Excellent service, food was expertly prepared -- really a wonderful, elegant meal in a beautiful location. A little more expensive than the Parrot Club, but well worth it. The salad with fennel, toasted pine nuts, manchego, and truffle oil was the best salad I've ever had. Halibut and shrimp main courses were delicious. Chocolate souffle for dessert wasn't worth the wait - and $12 was a little much for what equated to a rich brownie. Worth the trek to Santurce. If you go there for lunch, you can easily hop on the A5 bus to Old San Juan afterward.
Espana (Isla Verde) - a reposteria (deli/bakery) - excellent coffee, torta, cheesecake, empanadas - perfect place for a cheap breakfast/snack. Helps to know a little Spanish although pointing always works. The cheesecake was really good.
Dragonfly (OSJ, Fortaleza St) - I know it's not a chowhound locale, and I found myself getting annoyed with its manufactured "SoHo" (or SoFo, whatever they're calling it) vibe, but the fried calamari was really good. Is it me, or is it impossible to get a strong mixed drink in Puerto Rico? I don't think I had one the entire time I was there, and that includes Dragonfly. The mofongo tempura was creative and delicious, and the pork/plantain dumplings managed to be light and filling at the same time.
Baru (OSJ, Sebastian St) - food is secondary to the scene here, but at least it had great local flair, unlike the Parrot Club and Dragonfly with its fake "hipness," complete with ropes outside (please!) The lamb chops were pretty good and I liked the almond-goat cheese-mango dip with yuca chips.
El Pescador (at the Plaza del Mercardo in Santurce) - I wanted to love this place, but I thought every fish/seafood dish we ordered was overcooked. They had these great oyster things in a long, narrow shell that I've never seen before (does anyone know what they're called?) The Spanish name began with an "n." The marketplace is well worth a visit, but my favorite thing there was our batida inside the marketplace. My husband was thrilled - you can get them sweetened with fresh coconut juice and Splenda if you're avoiding sugar. Also helps to know a little Spanish here. You won't find a menu in English although our waiter was so nice and translated some stuff for us.
El Jibarito - Also wanted to like this place, but the only thing I liked were the sweet plantains (which were greasy, but delicious). My shrimp ajillo was overcooked (overcooked fish was the theme of my restaurant excursions) and the food was ready in like 2 seconds, and must have already been prepared. The mofongo was dry and tasteless. They were very nice there though.
La Bombonera - Don't understand the appeal of this place. It was packed at lunch and the only thing I thought worth ordering was the cream-filled pastry for dessert. The pernil I ordered was awful, but the rice sidedish was pretty good - it had beans, olives, ham, and peas. It had a name with a "j" (arroz con j__) but I forget what it was called. My husband had a breaded piece of fried meat called an empanada that was vaguely reminiscent of a school lunch. The cafe afterward at the Plaza de Armas helped make up for the meal.
The Parrot Club - I cast my vote against this place. Touristy, overpriced, loud. Food wasn't anything special (my halibut was overcooked although the nuevo latino ceviche was decent) and the service was rushed, rushed, rushed. Waiter kept pressuring us to order their watered-down mojitos. Did not enjoy.
All in all, I recommend Pikayo for a splurge, Espana for breakfast/lunch, and Baru for good food and a great bar scene. Stick to beers and wine, and be sure to visit Maria's for great frozen nonalcoholic drinks instead. The bartender there called Choque is wonderful.