Having extensively used the public transportation system in a number of US cities, NYC has been by far the best place to try to get around by subway. Is there another US city where you think the subway works much better?
Chicago's threatens to be borderline usable, but unfortunately as you tend away from the Loop to the vast expanses of suburbia, its utility diminishes exponentially. Still, by comparison to 95% of Middle America, Chicago definitely deserves a top spot.