Flagship Cruises & Events runs one of the best sightseeing and longest running harbor tours in San Diego. You could take a 2 hour tour that includes both North and South Tours or do as we did and do different days, with one hour of each.
For more info on pricing and where your tours take you, please visit Flagship Cruises & Events.
Note as well that they also run dining cruises, whale watching tours, have private charters, do the Coronado Ferry runs and can take you for a thrilling jet boat harbor tour on their Patriot Jet Boat.
This was a great one to check off the bucket list- the harbour tour!