Congrats on your upcoming trip! We'll actually be there too, but not until the very last day in May, through early June. Although our kids are a lot older than yours (18 & 15) we've been down in the area when ours were much younger! I would suggest
Legoland in Carlsbad, towards San Diego. It's along the coast, you can either drive there or take Amtrak. We're taking Amtrak to San Diego when we first get down there, we've done it before, and loved the experience. Our kids also loved Seaworld, they have all kinds of neat shows, including one with dogs and birds! There is a section just for little ones called "Bay of Play" that features Sesame Street characters. The beaches there are so nice and a lot are family friendly, we decided to stay on Coronado Island, and the beach there has been featured in the top 10 beaches on the Travel Channel! There's a really neat tour called the Old Town trolley tour, they will pick you up from different areas or you can drive and hop on. It's a hop on, hop off type tour, in a open air trolley. Very nice, they go to Old Town, Seaport Village (which has a carousel, restaurants and shops) Coronado Island, Balboa Park and more. Not sure what you would do in LA with little ones, it's such a big city, there are a lot of fun things to do, for instance, we took a tour near there in burbank and went on a VIP Warner Brothers Studios tour, but your kids wouldn't appreciate it at their age...Of course, there's Hollywood/Grauman's Chinese Theatre, but again, not sure if they would like it.
We did do a really neat tour called OC Wildlife & Beach tour. They picked us up from our hotel, it was a very relaxing time, got to visit a marine mammal refuge, she brought us to Laguna Beach where we wandered around the grounds of this beautiful resort and had incredible views of the ocean, you could walk down to the beach via wooden steps, it was just gorgeous! She also drove us to Newport and visited a park, and lastly a nature preserve with tons of different kinds of birds! It was such a nice way to end our vacation before heading home, especially after the hectic Disney schedule. I highly recommend it, you are the only ones on the tour, so very intimate, and Cheri (owner) is gracious and knowledgeable!