Don't leave Caye Caulker without a snorkeling trip, either all day or half day. My other advice is take a kayak around the island. I mean, paddle it yourself. It's a lot of work but great fun.
Snorkeling near the reef off Caye Caulker wasn't quite as spectacular as around Gladden Spit where I went in 2005, but it's still amazingly beautiful. Shark Ray alley is fun, but even more amazing is the "channel" in the Hol Chan Marine Reserve, where the bottom drops out and sudden you are looking down 60 feet at SCUBA divers on the bottom. The water is clear all the way down and it's amazing. Water in Belize is about 75-85 degrees F, so it's very comfortable to be in the water for hours. Take an all-day snorkeling trip and you will end up having lunch on Ambergris Caye. San Pedro is a cute little town but very touristy and it will make you appreciate Caye Caulker all the more. For a great all-day snorkel trip we used Anwar tours, which is right across from the ice cream shop and not expensive at all.
Fondest memory: Caye Caulker immediately feels like home and the worst part is leaving. It's like a small town but a GOOD small town full of interesting people and a very relaxed attitude. It's not fancy or rich but it's real. There's not much to do there, which is the point. Just look at the beautiful blue water, and let your mind wander. The food is great, (though not all that cheap) and the sunsets are gorgeous every night.
They do various sailing tours, we did the one day snorkelling trip to Hol Chan Marine reserve which was a fantastic day out and the snorkelling is very good ($40 and they did not charge for our 4 year old). Friends we met on the island did the three day trip from Caye Caulker to Placencia ($250 everything included), stopping at Rendzvous Caye and Tobacco Caye, they said it was a fantastic experience and the high point of their 6 month trip in Central America.
The Barreer reef is a paradise to both snorkelers as divers! And of course the tourist bureaus know that so the're plenty of choises exploring it. Expensive choises or cheaper. The cheapest you'll find (for snorkeling) is about $10 per person, but the most are more expensive. If you are in group you might get a reduction.
On your tour you might see plenty of tropical fishes, corals, dolphins, manatees, sharks, ...