NYC also closes train lines for weeks at a time for maintenance, whereas Tokyo never does so.
NYC switches train schedules after midnight to every 30m or 1h until 5 or 6. The schedules in Tokyo are at worst every 10m, but most are every 3-5m, or 5-7m until the last train.
There's tradeoffs both ways. I really like being able to get a train after midnight in NYC, but I somewhat prefer the frequency and consistency of the train lines in Tokyo.