Shared modes of transportation, paired with public transit, provide great benefit to cost of living on the individual scale, and to broader issues like air pollution and traffic congestion on a city-wide scale. In an attempt to simplify the use of the multiple services available to city residents, and hopefully provide incentive, these services should consider unifying fare payment systems by using software development kits (SDK).
In the way that Lyft drivers are guided by Waze for navigation, the MTA, citibike, Zipcar, and Lyft, can pool together a resource of funds for in-app purchases of metrocards, subscriptions, or rides.
For the volume of funds a system like this would require, it seems like the financial management would be best housed in a city government entity. The other parties involved would be responsible for app production and maintenance. Together staff members of each service would represent their organization’s interest and be the liaison between the joint venture and the support of their organization.