I'd like to offer some information on an option in Bonaire that we took advantage of recently, since I don't see hardly any mention of this on CC. It is chartering the 44ft yacht, "Amoray," of "Bonaire from the Sea." (http://www.bonairefromthesea.org) They do half day, full day, and multi-day outings, and they are suprisingly affordable, particularly for what they include. The primary staff are the husband/wife team of Rich and Sue Willis. He's a an expert snorkel/scuba dive instructor, and she is a marine biologist and gourmet cook (and diver as well). We had a lovely day sailing, diving, and eating with them. It was more like an outing with friends than a charter.
This was the perfect venue for us for a number of reasons.
We were concerned about uncomfortable seating out in the sun on a standard excursion. Not a problem on the Amoray -- comfort and shade. In fact, we had access to a cabin, bathroom, and shower if we wanted.
My wife was very nervous about snorkeling and needed one-on-one attention. Rich made this a wonderful experience.
We are foodies and liked the idea of quality food and drinks. Rich had us communicate our preferences/restrictions beforehand, and Sue customized her offering especially for us. Everything was perfection.
They took us for a leisurely sail (letting me try the wheel), then picked a dive site based upon wind and wave conditions. There were welcome aboard snacks, hot soup after the dive, a main course after that, and a farewell treat at the end. Drinks were available throughout, and not just of the canned/bottled variety :) This was the best day we've had in all our Caribbean experience. We will do this again if we come back to Bonaire, and it may well be what brings us back.