TBH, the answer is probably "all of them." I've been a few times now and done most of the tours as well as the ATX programme and "lunch with an astronaut." Out of all of it, the only one that was disappointing was ATX. The extended tours are well worth doing though.
The VAB is really interesting. Largest room in the world by volume, or some such. The launch pad makes for a much longer tour; I have a photo somewhere of me stood next to the countdown clock you see in launches on the telly. The other two I don't remember the contents of, I'm afraid.
Check the launch schedule. You absolutely need to be somewhere near satellite beach if there's one whilst you're there. We saw a rocket launch from something like four miles outside Minimum Safe Distance, and it's awesome in the very literal sense of the word.
Outside of the tours, the Saturn V room is something else. The rocket garden outside has a bunch of rockets on display, and there's (if memory serves) a Saturn 1B there. The 1B is so big they've had to lie it down, and the V makes it look like a firework.
Awesome place, I'm very jealous. Allow plenty of time to get there, it's further than you think.