The New York Times is reporting that New York City Transit's operating cost recovery ratio has reached 64.0%. I'll bet that recovery is far, far higher for the subway and lower for the bus; the separate MTA Bus Company (former private routes) only covers about 40.0%. Meanwhile, the Wall Street Journal reports that bus ridership has been going down since 2005, as subway ridership has going up. Bus ridership had been going down long term, too, before the free transfers with Metrocard caused a short term turnaround.
A variety of explanations is given for the fall in bus ridership. One that isn't mentioned is the increase in bicycle transportation. Take it from me, almost no one who has actually tried getting around by bike would choose a bus instead, unless they were physically unable to ride. Bus trips tend to be shorter than subway trips, either to the subway or in directions the subway does not go. Bikes are faster, given you don't have to wait for them, and no less confortable in inclement weather, given that wait for the bus is outside. And with the fare increases, biking is a lot cheaper too.