I don't know about the catamaran, but I know for sure that you can take them on the Catalina Express....the ferry. I think they limit you to one animal per person though...here's what it says regarding animals and I kind of doubt that you can take them on the glass bottom boat, but I'm not sure about that.....
Animals
Personal domestic pets are to be leashed and muzzled or in a pet carrying case while waiting to board the boat and for the duration of the trip. One pet per passenger. Pets are to stay close to the owner on the deck. Pets are not allowed in passenger seats or in the aisles where they may obstruct traffic. Pets must be secure in a muzzle, leash and collar or a muzzle and harness sufficiently strong and tight fitting to securely hold the pet, or the pet must be enclosed in a suitable animal carrier throughout the duration of the trip. Catalina Express will not assume obligations to store or care for pets at ports, docks or on board vessels. Animals must not have an offensive odor.
Here's the link to their website:
http://www.catalinaexpress.com/index.php