OK - I found some details. Took a while to remember - the trip we took was in 2002.
The very small "ship" was the Spirit of Adventure out of San Diego. They sail from H&M Landing. Most of the year it's a long range fishing vessel. But in the spring they to whale watching/natural history trips. They are still doing our trip.
Natural History/Whale Watching Trips | news
The organization we went through was the Oceanic Society. They contributed two outstanding naturalists to our group. This was a major deal - there was lots to see and identify from aboard ship! We also stopped at lot of outdoor islands and they led hikes. Natural history presentations some evenings. One of the naturalists did shark research off the Farallon Islands and was famous for his National Geographic documentary on the Great White Shark. The Oceanic Society does naturalist led small group marine mammal expeditions all over the world:
https://www.oceanicsociety.org/expeditions
It was truly an incredible adventure. The cabin was ridiculous - just room for a double bunk and enough floor space to stand in with luggage upright. I had to get over a bit of claustrophobia. But the galley and decks had tons of space. It was the most memory nature/wildlife trip we have ever experienced. And we have done a great deal of nature travel!
Hmm - it looks like the Oceanic Society is not doing that particular trip with the Spirit of Adventure anymore. They are offering this option for whale watching in Baja California:
https://www.oceanicsociety.org/expeditions/baja-san-ignacio-lagoon-and-sea-of-cortez--69