Assuming you don't want to go to the med school associated with your undergrad, your choice of school won't really help you or hurt you, reputation-wise. However, the fact that there is a med school there can make it easier to gain research experience or clinical experience, if you so desire.
School reputation is tricky -- some people associated with admissions committees *swear* that their schools give an automatic numerical "boost" to applications from certain elite universities. Other people insist that school name plays a very minor, insignificant role in the process. I think the bottom line is that you want to do the best you can wherever you are, and don't discount the importance of the MCAT. Assuming you have strong scores and a good GPA, you should be in good shape.