Chankanaab has lockers for a nominal fee.
I've never had a problem leaving my valuables on a boat during snorkeling excursions to places like Stingray City, but if you're the least bit concerned about it, don't bring your good camera. Buy a few disposables and use these while on excursions. Stingray City is a blast, so be sure you have a few underwater cameras.
Jamaica is another story. Leave your valuables on the ship.