Definitely go with 2nd Ave. Its cheaper, a bigger room, and IMO has a better location. You're 2 blocks from the front entrance of St. Mary's, which you will likely spend time at while you are there. If you are downtown or are going to the main campus for any reason, they have the free shuttle that picks you up at the front entrance to St. Marys (again, 3 min walk) and drops you off at the Front entrance of the Mayo building. The shuttle runs every 15 min and takes less than 10 min to get there.

I stayed at the Grand and it was fine, but parking (since I drove to Rochester) was an additional 7 bucks a day and it was just expensive overall. Small overall rooms but more than adequate for sleeping, showering, etc. Community kitchen on one of the floors that a lot of students used.