The National Research Council just released a 5-year, $4 million research effort to rank graduate programs in the U.S. - but no one seems happy with it.
Here's the story on the controversy from Inside Higher Ed, including a link to the study and a downloadable database of its information. You might be interested in what kind of criteria they use.
At least the problems show how difficult it is to rank such programs - in contrast to the way it might seem from the college rankings at U.S. News & World Report or others like it.