The age of the system also means that many of the tunnels are nearly 100 years old, and a lot of those fuckers are reeeeaaally filthy. It's crazy how ancient (and makeshift) some of them look. So the trains are running through miles of dirt, soot, brake dust, old bits of wood, brick, etc, whereas a lot of more recent systems have concrete tunnels that leave less debris on the trains.
Also, unlike many subways, NY's trains are running 24-7 (at least in theory, ha!) which leaves less opportunity to clean cars.