This is rather old news, but I just found out that Putnam Transit now operates the Croton Falls Shuttle, every since January 4, 2016.
http://web.mta.info/mnr/html/raillink/schedules/CrotonFalls_0416.pdf
http://www.putnamcountyny.com/wordpress/wp-content/uploads/2012/06/CROTON-FALLS-SHUTTLE-1-16-2.pdf
Now, this is new to me since there really wasn't much publicized about the swap in operators. Before, Coach USA Shortline operated the service. As to why Coach USA decided to end its operations of the shuttle remains unknown, but ridership and the overall cost may have to deal with why it was. IIRC, the Croton Falls Shuttle doesn't carry much of anyone, and it is a waste of resources. Or the MTA may have wanted a more efficient operation of the service, and they likely went with Putnam Transit, since their operations are within Putnam County already.
The Croton Falls Shuttle used to be a bus route operated by Bee Line bus, but then was transferred over to Coach USA.