I went there on a Carnival Cruise line and went out with this young guy and his cousin and they were AMAZING. They showed us around where the reef was and also took us to Shark Ray Alley. We went to essentially 3 different "carnival" tours. I wish I could remember his name. All you have to do is take the water taxis which is right down the road maybe a half a mile from the where the boat drops you off. It is well worth the trip and the people are all FANTASTIC.
You must go to Caye Caulker. I am itching to go back.