What US cities, at any time in their history, have had two or more MLB teams?

Chicago is one, being home to the Cubs and the White Sox.

http://www.encyclopedia.chicagohistory.org/pages/114.html

Chicago, Cleveland, New York, Philadelphia and St. Louis

http://www.baseball-reference.com/teams/

The Angels played in Los Angeles from 1961 - 1964, so you could add Los Angeles to the list.

http://www.baseball-reference.com/teams/ANA/

Boston would be another with the Boston Braves.

http://armchairgm.wikia.com/1914_Boston_Braves

And the Boston Red Sox.

https://en.wikipedia.org/wiki/Boston_Red_Sox

Detroit - Wolverines

The Detroit Wolverines were a 19th century baseball team that played in the National League from 1881 to 1888 in the city of Detroit, Michigan. In total, they won 426 games and lost 437 before disbanding, taking their lone pennant in 1887.

https://en.wikipedia.org/wiki/Detroit_Wolverines

Detroit - Tigers

The Detroit Tigers are a Major League Baseball team based in Detroit, Michigan. One of the American League's eight charter franchises, the club was founded in Detroit in 1894.

https://en.wikipedia.org/wiki/Detroit_Tigers

MLB teams are considered to be those from 1901, when the American and National Leagues were established, to the present. Before that, there were many teams with short-term affiliations with different cities and leagues, and many teams shared the same home town.

Originally (1901) Boston, Chicago, Philadelphia and New York had two teams. In 1902 St Louis got a second team. In 1903 New York gained a third team, the Highlanders, later to be known as the Yankees. In 1958 the Brooklyn Dodgers moved to Los Angele; the 1961 expansion which created the Los Angeles Angels made LA the 6th city to have two MLB teams at the same time.

http://everything2.com/title/Major%2520League%2520Baseball%2520Teams

Im no MLB expert but I found the following

The first year of the National League was 1876. The teams playing that year were from Chicago, St. Louis, Hartford, Boston, Louisville, New York, Philadelphia, and Cincinnati.

The first year of the American League was 1901. The teams playing then were from Boston, Philadelphia, Baltimore, Washington, Detroit, Chicago, Cleveland, and Milwaukee.

http://inventors.about.com/library/inventors/blbaseball.htm

If you interpret the question to mean that the two teams were there at any time, not necessarily at the same time, there are a lot more answers. In addition to the 6 cities from the 20th century which had two or more teams at the same time, we also need to add the following cities who have had two or more franchises, although not at the same time:
Baltimore, Cleveland, Columbus, Detroit, Indianapolis, Kansas City, Louisville, Milwaukee, Pittsburgh, Toledo and Washington.

If you also include 19th century franchises that are not considered to have been major league teams, the list gets even longer!

http://www.baseball-reference.com/teams/