Noah Kazis explains that up until 2 weeks ago, 2 of the 4 alternatives being proposed for the Tappan Zee included both commuter rail and some form of bus rapid transit. By October 11th, however, all transit had been expunged from the plan:
"And it remains unclear who ultimately decided to abandon the transit component. Some media outlets reported that the federal government made the call; others implied it was the state. The New York Times reported that federal officials pushed for the transit elements to be postponed, while Transportation Nation noted that Cuomo hadn't invited the MTA to his meetings on the Tappan Zee Bridge for months."
Thanks to Noah Kazis