It's not really accurate to call MCW a "community hospital." Although you won't get the research pedigree that you might in a proper university setting where there's a full graduate college across the street, the Medical College of Wisconsin is a medical campus built around a medical school, and therefore should be classified as an academic program, albeit a lower-tier one as far as the prestige rankings are concerned. Academicians in the Midwest definitely know about it and respect it as such.
I don't know enough about UNM to give the original poster any direct comparisons, but I'd agree with the thought that MCW's hospital has a fair amount of money and is therefore less dependent on residents. Pay is about as good as you'll get anywhere in the country, especially relative to cost of living. The culture runs pretty friendly, very Midwest-nice. A few things to be cautius about: one, if it matters to you, do be aware that the main campus is not in Milwaukee proper but in the western suburbs, so your access to the nice city nearby will be more limited unless you commute (and the VA is a nice drive away for your months there). Also a heads up that there are a few strange things going on there on a higher up level - there's been a faculty exodus from a few departments including Cards and Neuro. The IM folks want to be more academically oriented, but some elements in the administration want to ship them off to new satellite medical schools, and others want to acquire more local hospitals and become a regional network. Don't know whether any of that would trickle down to you as a resident, though. A few strengths that jump out at MCW include the leadership in the IM program proper (it's one of two or three places in the area where people will tell you that they picked it because of the PD), Immunology, and Neph, especially transplant-Neph.