I'd say it depends on what your goals are and what exactly the reputation is for...is this patient reviews? Med student reviews? General community consensus?
For example, if you're shooting for a surgical specialty or something relatively competitive, go for the site that will give you the most exposure and networking opportunities with your desired specialty. Another consideration is patient volume. If you're shooting for EM or IM and you go to a site with only a few low-acuity cases, you might miss out on seeing the breadth of pathology that is typical of the field.
Personally I tried to get into one of my school's few sites with a decent GME presence. IE, multiple residency programs where you get a sense of not just the attending life but of the actual training. At the very least, I'd encourage you to go to a site with at least one residency program so you have some experience with the hierarchy of academic medicine, considering that no matter what you will be a participant for the next several years.
All else being equal, go to the site that has the reputation for giving students the best evals.