We just got back from SeaWorld with our DS6 and our DD4, and I'm not sure 3 year olds would be able to sit and wait for the shows (the shows themselves are fun to watch and only 20 minutes long...but you have to show up at least 15 minutes early, if not 30, to get good seats for most of them). Otherwise it would be very fun...my kids LOVED seeing all the animals and fish, especially the penguins, stingrays, sea lions! We crammed in as much as we could and only saw 6 shows in between viewing all the attractions. So if you took things slower and maybe only saw 3 shows dispersed throughout the day, you'd be fine I think.
For that age I would recommend seeing Believe with Shamu, Pets Rule! (and for this you don't need to show up really early, maybe only 5-10 minutes early), the Sea Lions show, possibly the Dolphin show, and Shamu Rocks at night if they are managing well. However there is plenty to do without seeing all the shows anyway...lots of exhibits where you can get up close and hands on....and the Happy Harbor water park looked really fun. I bet my kids couldve played there for 2 hours at least, but we didnt stop.
There are only 3 rides at the park, however, and your girls wont be tall enough for them. There is the Skyride though that goes out over the bay that they might enjoy and would be able to go on, it costs $3 a person, I think? Or there is an arcade that is indoors with games n such.
I personally havent been to Legoland, but it looks fun and there would be plenty of little kid rides. Just keep in mind that there would probably be more waiting in line there than at SeaWorld!