Bringing up the rear at no. 291 is New Britain, Connecticut. Sorry, everyone in New Britain.
To discover exactly why you're already griping about the ranking, you can see the full list of 291 teams, plus breakdowns by category, as well as a Q&A with their panel of experts here. At their site, they also break down the list into separate rankings by large cities (Los Angeles, Philadelphia, Lexington, and New York City comprise the top four there), medium-sized cities (Durham, Norman, Ann Arbor, Cincinnati), and small cities (Chapel Hill, Bloomington, East Lansing, Lawrence).
While the whole thing is inevitably going to upset residents of 290 cities, there's always the tournament to make you feel better about everything.