Cruzdoc - the key thing that may rule your planning is water and Diesel availability. That can only really be had at Marina Puerto Del Rey in Fajardo.

When leaving from STT we plan a stop at Del Ray in the middle of the trip to tank up and buy more Heineken. It's also well worth spending two days there, renting a car and driving up into the rainforest (El Yunque) for a hike, and perhaps a day in Old San Juan.

Other random thoughts...

Anchor either in Sun Bay or off Esperanza, Vieques.
See the Bio Bay. Go with a reputable tour guide.

Culebrita is worth two days ... the Jacuzzi's and the lighthouse are worth a visit.

If you need provisions, the supermarket Isabella Segunda in Vieques is good, and the bus from Esperanza is only $4.

Esperanza has some great places to eat. We like Duffy's.

I'm told that getting the anchor to hold off Esperanza is difficult, but we've not had any trouble. Find a spot without grass between the shore and the western Cay.

Green Beach just south of Punta Arenas on the west end of Vieques has great holding in about 10-feet of water. You feel like you're at the end of the world there.

There is great snorkeling off the boat at Tamarindo Bay, Culebra.

If you are on a catamaran you can anchor in Flamenco Bay in the NE corner near the beach. Excellent snorkeling off the boat near the rocks on the east side. The surge in the Bay can make a monohull a bad choice here. Flamenco Beach is one of the most beautiful in the Caribbean.

Don't worry if there are lots of power boats in the anchorages you choose. They will all leave by 5pm. That gives you a chance to move the boat closer to the beach if you want.