It depends when you go. If you are going during the summer, what you can expect is the largest collection of Homo sapiens you have seen in your life. Sea World and the zoo are crowded almost to the point of being unenjoyable. HOWEVER, if you go in mid to late summer, both of these stay open late (zoo until 9pm and Sea World until 9 or 10pm).
Although I am not a fan of Sea World (last went about 20 years ago, left after half a day and would never go back), the zoo at night is a truly great experience. If you do not desire to stay from open til close (9am to 9pm), then I would suggest go for the first two hours (9am-11am), get a hand stamp, go enjoy lunch near the harbor and a rest at the motel (or one of the many museums next to the zoo), then return to the zoo from 4pm until close.
If you are not going in summer, then of course all of the above is irrelevant (but if you are going this Spring I would try to avoid weekends if you can). For the safari park, plan on staying from open until close and plan on LOTS of walking (very worthwhile walking). Again, a weekday is better than a weekend. If you want to see the cheetah run (very worthwhile), plan on getting there at least 45-60 minutes ahead to get a spot along the railing (unless you want to pay extra for the VIP viewing area, which includes meeting the cheetah up close afterwards).
Depending on when you go, the Safari Park will close at either 6pm or 7pm. However, if you arrange your walk to be near the bottom at closing, you can work your way back up and not be at the exit gates until almost an hour later - in my experience, they will not kick you out. Likewise, although the zoo closes at 9pm, you can stay in the front plaza well past that - the gift shop stays open until at least 9:30pm ususally.
If you want some less formidable animal attractions, there are a couple smaller ones in the area. Birch Aquarium is a nice small aquarium on an oceanside cliff in La Jolla (just north of San Diego). The California Wolf Center (or something close to that) is in the foothills just east of the Safari Park. If you really want to be adventurous, there is a small but relativley new zoo in Tijuana, Mexico.