I picked Chicago over Berkeley for math and computer science. I think for the majority of programs, you will find higher academic quality at Chicago, primarily because of class sizes and focus on undergraduate education. I was lucky to get enough FA at Chicago such that it was cheaper for me to go to Chicago over in-state Berkeley. If Chicago is something you can afford, based on my experience, I would strongly recommend Chicago. If you have to take on debt to attend Chicago, I would pick Berkeley.
On the pre-med side: The pre-med here at Chicago is very rigorous; I have a few friends doing it, and while they say its hard, they enjoy it. We also have pretty strong med school acceptance rates. I also have friends doing Bio + CS or Bio + Econ (not pre-med), and are working towards careers in the intersection of these fields (PM for details). If you are interested in grad school for chemistry/biology, I would also highly recommend the molecular engineering program.
Note: Even If you get transfer credits to Berkeley, I am pretty sure you will have to redo a lot of the classes because Med Schools require that you do. Be sure to double check this.