"Or perhaps horizontal tornadoes could roll through the New York subway system every night from 2-5am, cleaning out the underworld of its dust and potato chip bags"
This might be nice, except some people rely on the subways between 2-5 am (it doesn't help that most bars close at 3-4 am on the weekends). There are some periods where the trains run every 30-45 minutes instead of the every 3-5 minutes they do during rush hour, but they always run - so there would always be an obstruction. Subway tunnels are always blocked at some point, so this solution wouldn't really work to clean the tunnels.
If the tunnels were round and less historic, with smooth surfaces, it would be possible to build a robotic cleaning train. But with the current tunnels, there are just too many hidden surfaces for this to be worthwhile.