In San Juan, be sure to check out Viejo San Juan. I recommend Pannes and Waiter’s Gastro Bar for good food that’s reasonably priced.
Culebra has beautiful beaches and great snorkeling, so if you fancy those, check it out. You catch the ferry at Ceiba ($2), or you can fly from San Juan at greater expense. If you eat there, there’s Heather’s (pizza and pasta), Zaco’s Tacos, Mamacitas, and Dinghy Dock for good, affordable eats.
Culebrita – a couple miles off the east side of Culebra – is a great day trip for the adventurous type: hiking, multiple beaches, cliffs/baths, a lighthouse, and goats. Bring food, though – it is rustic. Absolutely lovely though.
ETA: If you decide to spend a night on Culebra, I recommend Palmetto Guesthouse. If they lack availability, Mamacitas Guest House works too – it’s just a little louder, with the restaurant downstairs.