I love the Train Museum in Balboa Park. While you're in Balboa Park, the grounds are beautiful to walk around. The Museum of Natural History is within steps and their exhibits are always wonderful.
Ruben H. Fleet Space Theatre is also within steps. Their exhibits are great and they have an I-Max movie screen.
I believe that when Balboa Park Museums have "free Tuesday" that all museums are free. If that's the case for you, check out these other museums they are worth seeing!
The zoo is actually maybe a 5 min walk from the train museum, and you will pass by Spanish Villiage, which is an artists enclave with lots and lots of artist studios featuring all kinds of art, including glass blowing. (which is really fun to watch if you are lucky enough to catch them working!) Also, as you walk toward the zoo, there is a Carousel and a (1/4 guage?) train that you can ride. It sounds dorky, but I've done it and it was good touristy fun.
If you walk in the opposite direction of the Zoo, there is a wonderful aeropace museum.
I often spend the entire day in Balboa Park, and don't get a chance to see it all. Have a wonderful time!