We took the 2 hour ride and saw the entire harbor (it is divided into north and south excursions at 1 hour each, for those with narrower interest and time availability). The north end goes by Harbor & Shelter Islands, Point Loma, and North Island Naval Air Station, and the south end continues down Coronado, under the Coronado Bridge and then back up along the ships at the 32nd St Navy Base. It can get windy out on the water, so be prepared with layers. Also, this time of the year, it may be sunny on the land, but you don't have to go too far out to be under the marine layer, and you'll definitely feel the difference in temperature. There's a bar with drinks and snacks, if you like. The narration is interesting and informative. All in all, a nice (if slightly chilly) way to see San Diego from the water.