It should be noted that Tokyo's subways do not operate between midnight and 5am. Having 4-5 hours of downtime every night dramatically reduces the complexity of infrastructure upkeep and cleanliness, and taxis pick up the slack for the night shift and bar/club crowd.

There are myriad reasons why Tokyo's metro outpaces (for one example) NYC in reliability and sanitation, but not having a 24/7 schedule is a big one.