I am a San Diegan and go to the zoo a lot, not usually in the summer, because of tourist season..but occassionally do. It is about equally crowded on Saturdays and Sundays. Some Saturdays seem a little less busy as locals tend to go more on Sundays..but it is hit or miss.
I don't go to Seaworld, so don't have any first hand knowledge of the crowds there..guessing huge!!
The zoo opens at, I think 9Am, in the summer and it doesn't get real crowded until about noon and the animals are much more active early in the day, so VERY worthwhile getting there at opening!! Don't miss the merry-go-round outside the zoo, just south of the parking lot. Fastest one I've ever ridden....even has the brass ring thing!!