I've done a harbor tour twice. Really enjoyed it tho my son wasn't as thrilled. I think it was Hornblowers tour. You can do 2 shorter tours or one combined. Maybe called north and south? The one goes towards the ocean and there are sea lions out there. The other goes under the Coronado bridge. Both are narrated and I thought very interesting.
Look for coupons sorry I don't remember where I found them but I've seen them in several places/publications.
Wear sunscreen, you won't realize the power of the sun on the water until you start turning red.
If you have a car and really want marine life try a whale watching tour at
www.danawharf.com
We saw whales, dolphins, sea lions, check the website and they list the whales they spot each day.
A quick trip to La Jolla and the tide pools will get you close up to all the little sea creatures is great fun for kids. You'll need to find out the tide schedule for the best time to go. There are also sea lions close by.
Also in La Jolla is the Birch Aquarium, this is one of my favorites. It's not huge maybe 2-3 hours worth. Amazing view over the ocean. Various shows like shark feeding, kelp divers, hands on area. Their website likely shows the schedule for the shows, some are daily, others only a day a week.