The Hilton in Mission Bay is right around the corner from Sea World. It's not really around anything as it's in the bay so it's really nice. You can also look at Hotel Circle, which as the name implies is an area full of hotels in the Mission Valley area.
I would point out that you'd pretty much need to drive to SeaWorld anyways. It might take you 5 minutes to drive there from Mission Bay or 15 minutes from elsewhere.
We stayed at the Hyatt Regency La Jolla at Aventine. Really nice place, and only took us about 12 minutes to get to SeaWorld since it's really close to the freeway.
We love the Catamaran Resort--on Mission Bay, has lush tropical grounds, it is a bird sanctuary, has a beautiful, calm, clean beach out the back, and is right across the street from Ocean Beach, if you want waves, action, etc.
Maybe too late, but we just stayed at The Dana on Mission Bay which is right next to Sea World. You could walk it if you wanted, but they run a shuttle a few times a day. The Dana was lovely! Particularly the newer bay view section.