There's a thrift shop on West 17th that very occasionally has them. A few years ago I was there and found a large box with dozens and dozens of Playbills going back to the 1960s (Skyscraper and others). They were all in pristine condition and being sold for $1 apiece. I've seen them selling Playbills and programs other times but with no regularity. It's a thrift shop and they only have what people donate.
It's run by Housing Works, an AIDS charity, and located on the north side of 17th a few doors in from 7th Ave. They have a few other locations in the city but I can't remember them. Again, it's not a regular thing but if you are ever in Chelsea, it might be worth checking out.
ETA, I just reread your original message and realized you already know about Housing Works but the West 17th store, being a formerly gay neighborhood, probably gets more of this sort of thing than some of their other locations.
Updated On: 6/2/17 at 10:26 PM