2 questions:
1) If only 1 day available, San Diego Zoo or Wild Animal park, which one to go? Will go with my 5 1/2 yr old son who is active and outgoing type.
2) Any suggestion which beach area in SD to go with my son?

At the Wild Animal Park, he will be in your vehicle and the animals might be quite far away. For a young, active kid, the zoo would probably be a better fit.

The Zoo - HANDS DOWN!

the zoo is a lot of walking but is great. they have a tram ride which is good for kids (extra cost). the zoo take all day. they usually have a few "shows" during the day. get that schedule and that's a good time to sit down and rest.
the wild animal park is a combination of walking around and a 40 minute (?) tram ride around the park. you see the animals in the open which is rather unique.
both are good. the zoo will be a little more exhausting by the end of the day. the hippo and polar bear exhibits are wonderful.

beaches for that age - i'd choose mission. it get rather busy but lots of places to rent boogie boards, lots of eats around, lifeguard on duty during the summer, large parking lot. or, if you want less busy, coronado is nice.

I agree that the Zoo would be more fun for you and your son. The best beaches for small kids are La Jolla Shores, Coronado(by the Hotel Del), Torrey Pines State Beach and Del Mar. All have lifeguards.

The best beach for kids is the left side (facing the ocean) of La Jolla shores but go during the week as weekends are way too crowded. The other beaches mentioned have more rip currents and bigger waves. LJ shores also has a playground and grassy area. Also I'd pick the ZOO. The wild animal park is too hot in the summer.