If you book through travelocity, you can stay at the Ramada Limited Sea World for $53 a night, but if you book 3 nights or more, the rate falls to $43 per night (plus taxes plus fees). This includes two double beds, and the hotel is less than 1 mile from Sea World and less than 2 miles from Ocean Beach and located on a fairly busy street that has a Chuck E. Cheese, Denny's, a couple of upscale Mexican restaurants, a Chili's, a Panda Express, and an Olive Garden all within walking distance, and is a short drive from Shelter Island--a well known hotel/restaurant area.
P.S. The Super 8 is also reasonable, and is in the well-known "hotel circle" area. It is a bit farther east (farther from the water and from Sea World), but would also be a good choice. If you want someplace with a bit less traffic, go Hotel Circle and Super 8. If you want someplace with more restaurants close by, and closer to Sea World, choose the Ramada Limited.
Enjoy