This wasn't always the case as that only became noticable once SI got their NG Hybrids back in the late 2000s. Before that, people often complained about dirty buses, loads of breakdowns, missed trips, and just bad upkeep in general.
In my opinion (based on observation, only doing NYCT Depots):
Brooklyn: Grand Avenue and Jackie Gleason are the best while Ulmer Park (and to a lesser extent, Fresh Pond) would be the worst.
Queens: Casey Stengel seems to be the best overall one and it's not even close.
Manhattan: MJQ and MHV has many lines that go through parts of the city with money and as such, their buses are rightfully up to the task, and they deliver. MCH isn't bad either.
Staten Island: Charleston , as it's basically the CMF for SI.
The Bronx: West Farms is alright, but the others are just terrible.