Your cruise ship will offer both these tours. On most ships, the cave tubing trip is the #1 most popular shore excursion and the snorkel trip to Shark Ray Alley/Hol Chan is #2 (Altun Ha ruins are usually #3).
While you can do these trips independently, if you go with the ship's tour you may get priority tendering (the Belize harbor is too shallow for big ships to dock at the piers), which can save you a lot of time. Also, you are guaranteed you will be back on time.
But there are tours offered at the Tourist Village, and for the snorkel trip you can take a water taxi to Caye Caulker or Ambergris Caye, or a flight from Municipal, and then arrange for a snorkel trip, but frankly you will probably end up paying as much or more than if you go with the ship's offering.