Yeah, the Discovery Science Center will be fun for them. Or San Diego Zoo. You can take them to see Monsters University in 3D at The El Capitan.
If they are into sports, you can go to a game. My girls are 4 and 2, and love going to baseball games! Plus, Dodger dogs and chocolate malts...heck yeah!
Long beach aquarium, the tar pits, science center to see the shuttle (get tickets before!), do they like sports? Toyota sports center to skate (kings, lakers and clippers train there.)
Lurking from April 2012 but live in the area. There is Splash Water Park in La Mirada that is small but fun. Perfect for that age and much cheaper than the big water parks.