In his state of the city address Tuesday, Johnson said a new agency called Big Apple Transit should be formed.
It would have a board made up of New Yorkers who use the mass transit system.
He says the city council would have oversight over Big Apple Transit and it would have an independent auditor.
Johnson says the mayor would be responsible for its operation.
Right now, the MTA controls the fares, what gets built, and what is purchased.
"Municipal control means we decide how our system is run," said Johnson. "We decide how we raise our money, and we decide how we spend it. Municipal control means saying goodbye to the MTA."
Currently Albany is grappling with congestion pricing, which would put a toll on every car south of 61st Street, and all the money, about $1 billion a year, would go to the MTA.
Johnson warned that if the Albany doesn't pass congestion pricing, the city council will.
"The council has the authority to pass a local law to toll our roads and we're prepared to do it," said Johnson. "We need it with speed cameras and we have to, we will do it again with congestion pricing."
He says money from an increase in business taxes and money from the sales tax will fund transit reform.
Former MTA Chairman Joe Lhota praised Johnson and said that the mayor should run the agency, not the state. "I thought it was realistic in 2013 when I proposed that same thing," said Lhota. "I think it's realistic today. It's gonna take hard work."
The problem for Johnson in what he's proposing is that the future of the MTA is up to the governor and state legislature.
A spokesman for Mayor Bill de Blasio released the following statement:
"A City takeover of the subways is a worthy discussion that in a best-case scenario would take years to achieve. While he appreciates the Speaker's transit vision and contribution, the Mayor is focused on immediate actions to fix the broken subway system. Our subways are in the middle of a crisis that needs an immediate solution. The Mayor stands with millions of riders depending on action right now. We have four weeks to deliver sustainable revenue sources capable of turning this crisis around."
The MTA also issued a statement:
"The MTA's new leadership team has been working hard to deliver significant service improvement, cost reduction, and general modernization on all fronts. The recent data showing subway performance is at four-year highs, after more than $800 million was provided through the Subway Action Plan, is a perfect example of the type of progress we can achieve with a reliable funding stream. As we continue our serious drive to embrace innovation and contain costs, and numerous other initiatives to reform our business practices, we are laser-focused on the passage of congestion pricing and obtaining the funding we need to deliver the transit system that New Yorkers deserve."
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