NYC is dirty city. When there's trash on the streets all the time its hard not to feel like everything is dirtier.
That being said, I feel like it depends on the stations. I would argue that the dirtiest stations in NYC are way way more gross. You got some pretty gnarly rat situations in some of the stations.
NYC subway may be better in other aspects but as a New Yorker, I agree with parent that DC system is way cleaner than NYC.