Everyone love the views of downtown you can get from a San Diego harbor cruise, but you'll also get a peek at the Pacific Fleet - and a harbor cruise is the best way to get a feel for just how tall the Coronado Bridge really is. The bay is well protected and the water seldom rough.
The cruises make two out-and-back trips, one toward Point Loma and the other past the Coronado Bridge, the Navy Seals Training Base and military ships. The boat stops at the dock in between, making it easy for you to take just one leg or both. Opt for a brunch or dinner cruise and you can see it all while having a nice meal.
Harbor cruises leave from the waterfront near downtown, near the big cruise ship terminal. If you're getting there from somewhere else, the San Diego Trolley stops three blocks away at the Santa Fe Depot.