Erin,
My husband and I stayed a night here: http://www.oldtown-inn.com/ and it was very reasonable. Not fancy but clean and well located. They offer a free nice breakfast - homemade waffles - YUMMO and have an outdoor swimming pool. FROM THE WEBSITE:
Within walking distance of the Inn, you will find Historic Old Town, California's most poplular State Park, featuring restaurants, shops, museums, and artisans. Accross the street, at the Old Town Transit Station, you can take the trolley to downtown San Diego, the Convention Center, Qualcomm Stadium, world-class shopping, and the exciting city of Tijuana, Mexico. The Old Town Inn is just 2 1/2 miles from Sea World, and less than 3 miles from the San Diego Zoo, Balboa Park, Downtown, and miles of beautiful beaches and shopping.