Taking a Hornblower Cruise is the perfect way to see San Diego. We went on Memorial Day and had a fabulous time.
We were joined by many other tourists and families looking for a better view of the San Diego Bay (they have a North and South bay tour and we just stayed for the North tour – easier with our baby).
We enjoyed a professionally narrated tour of many landmarks from the sea. 
We covered over 13 miles on the Big Bay, passing by Seaport Village, Shelter Island, ship-building and dry-docking facilities, Coronado Island, Point Loma, and Cabrillo National Monument, among many others.
The narrators point out marine animals and birds.
We found many opportunities to take photos and see a new perspective of this big city.
I recommend getting a seat at the top of the boat but everywhere on the boat has a nice view.
The washrooms are on the bottom floor and can be quiet tight but just leave your stroller in the front room.