Take pre-reqs before MCAT.
Think about it. If you did the pre-reqs first, you'd understand/already know most of the MCAT content. Thus your studying would be easier.
If you don't do your pre-reqs first, you'll be teaching yourself the material as you study for the MCAT. Studying would be harder because you also have to teach yourself the material first. An extra step that may hinder your score.