We took the north and south bay tour, for a total of 2 hours. Went under the Coronado Bridge, saw the San Diego skyline from the water (awesome view), and he naval shipyard. The narrator was excellent and informative. A good time to just sit back and enjoy the sunshine.
We sat on the top deck. There is some inside seating, but I could feel the motion of the ocean from inside. Outside was perfect if you are a little queasy.