Hi!
First of all, I have to say that both the zoo and the Safari Park are absolutely full-day parks. If you go to either with the intention of only staying a few hours (which sounds like what you plan to do), then you're going to miss large, large portions of the parks and I'd question if paying the admission is really worth it in those cases. I actually work at the zoo and I still can't claim that I've seen absolutely everything, that's how big it is.
That said, I'll describe to two places and let you go from there.
The zoo, as you know, is in Balboa Park. Parking for the zoo is free. I will give you the disclaimer that there is currently a construction project happening at the zoo which affects the reptile area and the Australian Outback area. There are lots of construction fences, but still most of the other exhibits are open. There is a 35-40 minute narrated bus tour that covers about 70% of the park, and then you can go back and explore the other areas that you may be interested in.
The Safari Park is about 45 minutes north of here in Escondido. It focuses primarily on African and Asian animals in a more open setting. There is a tram that takes you through the main exhibit, but there are also lots of footpaths that will take you to see other exhibits, such as the big cats, the elephants, and the large raptors. Parking at the Safari Park is $10.
Both are awesome parks. I'd make your decision based on what types of animals you want to see and what type of experience you are looking for. Both parks require a LOT of walking and have a LOT of hills. Some animals unique to the zoo that you won't see at the Safari Park are the pandas (we are one of only four zoos in the country that has pandas), polar bears, kangaroos, camels, sea lions (in the sea lion show), grizzly bears, and several types of primates (other than gorillas, which are found in both parks). The zoo has more animals and a larger variety of animals, whereas the Safari Park has several different types of animals living "together" in one big exhibit (and other smaller exhibits throughout the park).
Neither will really be crowded on the days you mentioned, but again I want to stress that you shouldn't go to either park if you're in a rush to be somewhere else - such as the airport. They are both HUGE facilities and unlike smaller zoos around the country, spending two or three hours just isn't going to cut it if you want to have a worthwhile experience!