Tarzan's Treehouse is also a great place for little ones to just run around and play and chill out a bit. My kids LOVED it when they were younger. We spent over an hour on it the 1st day, and we had to stop every day after that, too. Only negative is that you're "supposed" to stay with them, which is a lot of climbing stairs, etc, lol. So you may not get much of a break!
Second Tom Sawyer's Island, but be prepared that there are very tiny cave tunnels, and kids can get lost super easily. We got separated from our DS last time we went, and even though he was older and I wasn't worried about his safety, it took FOREVER to finally find him so we could go do something else. Its quite a big island, and lots and lots of little hiding places!
Also, a ride on The Sailing Ship Columbia is fun and restful. Lots of places for him to explore below the deck, and fun secret things to see behind the island.
And a ride on the train is super nice! If you've never rode it all the way around, you totally have to! Lots of fun things to see "behind the scenes" (dinosaurs!!) It takes awhile to get all the way around, and its a great way to relax your feet. Buy him a drink and a snack and kick back.
Redwood Creek Challenge is really cool, too, and plenty of benches for mom & dad to sit down while they play.