Having extensively researched my quick trip to San Juan on chowhound and finding, well, not a lot of information for or against certain restaurants, I thought I would add my $.02 since we had a phenomenal gastronomic experience during our 3 days there.
First day: Arrival, bags down at La Concha (very nice place to stay in Condado!) and then off to Aguaviva (http://www.oofrestaurants.com) in Old San Juan. Had a lovely mojito, shared two ceviches (truffle tuna tartare and chillo y aguacate fresco) which were fresh and wonderfully marinated, and tuna wraps and salmon club sandwiches which were fresh as well and absolutely delicious. Service was not indifferent (saw this comment in a number of previous reviews?) and it was an impressive start to our culinary adventures.
Dinner was at Marmalade (www.marmaladepr.com) right across Fortaleza from Aguaviva and wow - what a meal. I can't begin to list all the sublime dishes the 3 of us tried because we all took advantage of their 5 course tasting menu ($69!) and tried, um, everything. First off, the restaurant was super quiet because its still slow season but its beautifully decorated (appreciated the high back chairs!) and the service again, very attentive. Stand out dishes: their famous white bean soup which was sinfully amazing and sprinkled with pancetta dust - does life GET better?!, the gnocchi with short ribs and wilted arugula (outstanding!) and a lobster risotto essentially simmered in lobster bisque. A few dishes were fine, good and the rest were exceptional; no mediocre food on our table that night. Very reasonable wine list. They were hyping their sister restaurant, Jam, but we opted out after reading numerous mixed reviews. Marmalade, however, is definitely worth a visit.
Second day: Breakfast at the hotel and quickie lunch at the pool. Dinner was at Dragonfly (sister restaurant/same group as Parrot Club and Aguaviva) and food was pretty good here - nothing jumped off the table at us but we ordered some very nice dishes. Worth mentioning were the peking duck nachos and rock shrimp tempura tacos; forgettable were the shrimp and lobster dumplings and the Latinasian veggie rolls. These four dishes were plenty of food for 3 girls but our absolutely lovely and gracious server (whose name I cannot for the life of me remember - but she was delightful!) talked us into dessert and the banana almond crispy wontons were a wonderful finish. I don't know that I'd go back - the food wasn't the caliber of Aguaviva or Parrot Club, but it was a lovely dinner.
Third day: Lunch in Loiza - fried foods on the beach. Really wonderful - no idea what we ate but anything fried eaten on a sandy beach under a blue sky is heaven on earth. We planned to hit Pikayo for dinner in its new location at the Conrad Condado Plaza Hotel but sadness of all sadness - it hadn't yet reopened. So we punted, and on the recommendation of multiple friends, went to Chayote (http://www.chayoterestaurant.com/home...) which was really, really something special. The wine list is extensive and reasonably priced and the waiters exceedingly polite and helpful. Immediately upon being seated, our white napkins were whisked away and replaced with black (little black dresses!) without a word - classy. Our waiter talked us through his recommendations as well as the specials and split each and every dish - without our requesting it - 3 ways. Very lovely service.
We began with a few amuse bouches (sadly cannot recall what they were - something heavenly with brie and something else...) and progressed into appetizers. We had the arugula salad with pancetta, goat cheese and papaya (aMazing), the prosciutto, tomato, spinach and gouda cheese Chayote (aMazing) and some special appetizer which for the life of me I can't remember. Also aMazing. Entrees were the angus filet of beef and the yellowfin tuna - both beautifully prepared and executed. I'm fairly certain we ran out of room before dessert although I know we ordered something...I just can't remember what. The food was outstanding and I'd absolutely return, especially to try the tasting menu.
Final day: Lunch at Parrot Club, back in Old San Juan on Fortaleza. Started with the corriander spiced crab fritters (quite nice) and the rainbow ceviche which was not as memorable as those at Aguaviva on our first day. I had the nuevo cubano sandwich which was VERY good (VERY salty!) and huge; my friends had carne frita (REALLY good!) and the grilled chicken wrap which, I believe, was actually fried and not grilled. The food was very good, service totally fine - I'd readily return for dinner there.
Overall, we were VERY impressed with all the meals we had during our stay in San Juan. No traditional Puertorrican meals - mostly fusion and so on - but lovely selections all of them.