We went to San Diego in May with our 3 year olds and Sea World was a huge hit. The Sesame Street part wasn't open yet, but we still go to do Breakfast with Elmo (and Bert, Cookie Monster and others too) and they loved it! We also did a dinner Shamu one night and it was great, but if I was to do it again, I would do the lunch instead. It is cheaper and just as neat. Sea World is full of lots of shows, but mine enjoyed the shows, especially the "Pets Rule" one. We spent three days at Sea World, a few hours here, a few there, etc.
Then we went to the zoo. The zoo is on drivable streets. It is only the buses that drive through, but they are coming though literally once a minute. Since you have kids in a stroller, you will have to go up and down curbs, not to mention the kids will likely be too low to see into the animal enclosures. And you will be fighting other stroller parents for space on the side walks. We got a bit irritated after 45 minutes and only getting to the elephant and giraffe section so we got on the tour bus, took the 45 minute ride (which we liked) and went back to the cottage.
Honestly, the zoo was gorgeous, but I don't think it is good if you only have one day or children that are reliant on strollers.
Given a choice, my kids chose to go back to Sea World vs the zoo. Make sure feed the seals, go to the Pets Rule show and to see the polar bears. They have real snow on one of the walls there that the kids can touch!
Have fun and feel free to pm me if you have anymore questions. It is all still fresh in my mind.