Do you have a masters?
I don't know about the sciences, but in the humanities, look at the sub-disciplines within the larger field you're interested in and you'll probably be able to ID the 4-5 schools that focus in that area. You'll also want to look for scholars whose work you're interested in and could serve as a mentor & dissertation committee person. After doing internet research and phone calls to the department chairs, I'd highly recommend making visits to 3 or 4 potential schools. Getting to sit in on classes and talk with current students can really help figure out which school would be the best fit.
If money's a consideration, some schools might be able to make stronger offers (assistantships, in-state tuition wavers, etc), which could help make up your mind.
And the Midwest is a fine place with many top-notch institutions, so don't rule it out. Once you're done with your coursework (2-3 years), you can go back home and write your dissertation.