The key sentence follows:
Those who only use the bus are more likely to be older and poorer, with a median income of $39,600, than those who use the subway as well, according to a 2014 MTA survey.
I bring up that sentence for the reason for the drop may be economics in the sense that people have opt for other means of transportation over buses.
New York City is NOT a car friendly town (to many people), thus automobiles are not a real options for most people when it comes to going to and from work (even if they own a car). The article mentions taxis and uber, but then bicycles but ignores people opting to walk.
The comparison years, 2014 and 2009 are five years apart and in 2009 the US was still recovering from the recession of 2008 (and it was a "Jobless Recovery"

. In the cases of lower Income people the options are limited, mostly to walking. Given the drop in ridership is restricted to buses and people who ride buses (according to MTA) tend to have less money then people who take the subway (and subway ridership has INCREASED in the same time period) makes this sound like a working class and poor change not among the Upper Middle Class.
Thus several explanation for this drop MAY be the case:
1. The poor and working class has undergone a drop in jobs so they no longer have to travel to and from work anymore (i.e no money for bus fares, or rent for they have no income).
2. To save money the poor and working class have decided to walk to work or the subway stop.
3. The poor and working class have opt for bicycles (Not supported by surveys but possible).
4. The poor and Working class have moved outside the city in search for work.
I would like one of the above be the solution to why the drop, but from what I can read no one knows and that makes this drop worse. If you know the cause, you can address the cause, but if you do not know the cause, you can not address the cause. We need more data, including why people have stop riding these buses.