Make note that the residents of the cities have nothing to do with the ensuing city battle. They're like grains of sand falling off of the colosi and have no effect on the match.
I'm going with San Francisco, cause it's got that pointy pyramid building to use as a knife.
San Francisco would absolutely win. It could use the Golden Gate Bridge as nunchuks. Then it could use the Bay Bridge as a whip. The Transamerica Pyramid would definitely come in handy, too.