I think Philadelphia had a Republican machine. EDIT: I think that either Nassau County or Suffolk County did too.
Plus, probably some historically Republican cities like Cincinnati, assuming Cincinnati ever had a machine.
Boy did Cincinnati have machine politics; from my understanding it was one of the most reviled of the urban machines from the viewpoint of the muckrakers and civil reformers. Boss Cox ruled Cincinnati with an iron fist from the mid 1870s to his death in 1916 and kept Cincinnati a Republican controlled city throughout his reign. Other than Cincinnati, Philadelphia's GOP apparatus was arguably the more dominant of the two party machines in the city up until the 1940/1950s. Chicago switched back and forth between Republicans and Democrats until about the 1920s when the Democrats finally shut out the Republicans.
Generally speaking though, urban machines were largley Democratic affairs in the big cities because machines were usually designed to cater the most heavily towards the Democratic base in the North: immigrants. Republicans obviously had their own problems with corruption, but Republicans were also the party of progressive reformers, the middle class, and Anglo-descended nativists, all of which had their own reasons to despise the urban machines. They also didn't tend to pack as heavily into the cities in the North to the degree that Democrats did and were thus not in as much need for extensive urban patronage networks.
