Tip of the morning:
Bio Bay on Vieques is a must see!
It is a spectacle of the world. There is literally nothing like it anywhere else.

If your group is fit, the kayak tour is the way to go.
If you're not so fit, the electric boat tour is the way to go.

Whatever you do, PLEASE pick a reputable tour. I'll digress for a second... Our first time we picked a not-so-good tour, and our guide almost killed himself (I'm being totally serious). First he didn't get all the kayak's tied up properly in the middle of the lagoon, and one floated away. Then he started swimming after it (with paddle in hand) as it was being driven rapidly by the wind to the other side of the bay, a half mile away. Third he didn't wear a life-jacket, and after he became exhausted he began to drown. Remember it's pitch-black dark, too. All our remaining kayaks were tied together, and he had my light (he forgot his). Two fit people from our group swam after him with life jackets, and we finally got a kayak loose. They saved him. The worst part was that he had the bus key with him, so if he had drowned we'd have had to walk back to town. <img src="http://www.traveltalkonline.com/forums/images/graemlins/duh.gif" alt="" />

So do your research, and choose wisely!