It's the refs for sure, most likely top of the food chain with only a few liaisons/officials working with the refs. They're not told directly, but they get the idea of who the league wants to win.
I don't know why everybody is ripping their hair out trying to figure out how it's done. Donaghy spilled the beans to the FBI about exactly how it's done. Easy to find the details if you Google. The FBI believed it enough to reduce his sentence.
The reason the FBI didn't investigate the NBA further is simple, IT"S NOT ILLEGAL TO FIX GAMES, it's only illegal if there is gambling involved. Otherwise the rules are the same as WWE, it's entertainment.