I would plan on two days since the water park will be open. We went for one day in April a couple of years ago and did not get around to seeing everything, and the water park was not even open at the time. The Beluga show was really neat, and of course, you have to see the Shamu show. We missed the water skier show (my daugher wouldn't leave the kids play area), but it looked neat. There are lots of smaller rides for your three year old and a whole area devoted to younger kids.
Eat before you go. The food is expensive and the lines at all of the food places were crazy, even in April. I imagine it will only be worse in June. There is a bakery to the left of the fountain after you enter (if I remember correctly). They had pretty good coffee. They also had pastries, muffins, etc. The prices were not outrageous and the line was non-existent first thing in the morning. We got hungry, but just fed my daughter goldfish and stuff and went out to eat afterwards.
As far as where to stay, just remember that the Riverwalk is a fairly large distance from Sea World, but the prices to up the closer you get to Sea World, so the savings might be worth a little bit farther of a drive.