I'm not sure what you mean by clinical medicine, but I think they'll all train you well.
I think UVM is always towards the top in primary care rankings, although I don't know if they are at all meaningful. I also remember hearing that they have one of the higher student happiness rankings, but don't quote me on that.
Beyond that, I think the prestige goes roughly UVM - AMC - NYMC. The practice settings and towns are really different. You might want to consider where you rather live as well