There are several independent companies offering tours of Roatan. There are also several major shore excursions companies that offer tours as well.
We much prefer this way to book excursions than booking through the cruise line - much easier, cheaper, and a whole lot less crowded and regimented making for a more enjoyable experience.
With that said, West Bay Beach has some of the best snorkeling I've ever seen around the world. So if you're into snorkeling or scuba diving, try it there as it's awesome!