You might want to check out Java Mama, a cafe designed for families with young children. They are re-opening on May 5th after a recent move. The new address is:
9880 Hibert Street
San Diego, 92131
I haven't been to Legoland, so I can't help there. But last time I went to Sea World, I did find a nursing room near the Bay of Play. I have also nursed my dd as she stood in the stands during the dolphin show. I used a nursing cover, and I didn't notice anyone saying anything, but who knows? I have also nursed her in some of the darkly-lit aquarium buildings, which is a bit more private.
As for museums, I know there is a children's museum downtown at 200 West Island Avenue. http://www.thinkplaycreate.org/
As the pp said, Balboa Park has all sorts of museums: art, science & technology, sports, even a model train museum. Reuben H. Fleet has a science-educational play area for kids, and an IMAX theatre. There is also a puppet theatre, if your kids are into that. So you can probably find something at Balboa Park, depending on what your family's interests are.