The Marieta Islands (Islas Marietas) are located just outside the northern edge of Banderas Bay. There are a few tour operators who go there from Puerto Vallarta and possibly one or two from the northern peninsula (Punta de Mita) area. It's about an hour ride by catamaran from Puerto Vallarta. The islands are a serious bird nesting ground.
The islands are volcanic in nature and thus have some interesting rock formations. These were - one might say 'enhanced' - in the early part of the 20th century when the Mexican army used it for artillery testing. Since 2005 the islands have been a national park and thus the military and whaling history of the islands are not emphasized.
Along with pelicans, terns, gulls and frigate birds the islands are home to boobies as well. In particular both the blue-footed booby and the brown booby live here. You can't get particularly close to the nesting grounds but with a good zoom lens or binoculars there are some bona fide blue feet out there to be spotted.
We went with Vallarta Adventures which has both pros and cons. On the plus side they're professional and competent and they give you a choice of several activities including diving, snorkeling, kayaking and just sitting around on the beach. They also make some excellent limeade. On the negative side you have to deal with the greatest party hits of the past 30 years on the ride back (complete with conga line).
This was our first experience snorkeling in the Pacific Ocean. It is downright cold compared to the Caribbean / Gulf of Mexico. The water in April was about 72 F (22 C). The visibility is also not quite as good as other places we've been but to be fair it was also an overcast day.
I don't think it's really encouraged to handle the fish - in fact we didn't. But a puffer fish made the mistake of puffing in the vicinity of all these snorkelers and apparently it takes them a while to deflate back to swimming buoyancy again.
We kayaked as well and the shoreline has hundreds of little coves, arches and caves to explore. Some of the information on the national park claims that humans are not allowed to set foot on the islands. If that is true it's not particularly well enforced as most boats that visit the island shuttle people to one of the 'beaches'.
We could've spent a lot more time kayaking actually. In spots the water is clear enough that fish, starfish and stingrays can be seen easily from the surface. Despite the crashing waves against the rocks there were not a lot of difficult currents between the two larger islands where we spent our time. Between the waves and the several hundred sea birds around every cove it is not a quiet place to explore.
Whales that frequent the bay in the winter had moved on by the time of our visit in April. Spotted dolphins live here year-round in large pods. This group we saw out in the middle of Banderas Bay had probably about 50 members. The un-spotted spotted dolphin on the left side of this picture is a young dolphin calf. Apparently they have to grow into their spots.