I initially decided to let one of them bunk in the living room for free because the futon is uncomfortable but since they have been great roommates - he brings the garbage down and keeps his floor really clean, I don't want to charge them for overstaying. I am not taking any money from them secretly. Is that okay with airbnb? They are both legally monthly roommates in NYC after one month.
Sounds like you are operating completely off the AirBnB platform and there is notning wrong per se with that - particulary as it is some one you know and trust.