The plan, which must be approved by the state legislature, marks the first time Governor Andrew Cuomo and Mayor Bill de Blasio — both Democrats — have set aside their bitter differences to support a comprehensive upgrade.
With six million passengers a day, the system is the largest in the United States and one of the world’s most heavily traveled.
But its many failings — delays, overcrowding, accidents, filth — have long been a source of political discord and growing rider discontent.
De Blasio wanted a “millionaire’s tax” to finance modernization, and has regularly blamed Cuomo and his state transportation authority for the subway’s decline.
Stressing that the crisis “runs deeper than ever,” de Blasio acknowledged that “among all alternatives, congestion pricing has the greatest prospects for immediate success.”
Under the plan, electronic tolling devices would be installed on roads on the perimeter of Manhattan.
Vehicles entering the “central business district” would be charged cashless tolls that would vary according to congestion levels, with off-peak discounts. Emergency vehicles would be exempted.
A similar system has been in place in London since 2003, as well as other big cities like Singapore, Stockholm and Milan.
Revenue from the tolls, and from a new internet sales tax, would be used to revamp the subway.
Cuomo approved a $1 billion emergency plan in 2017 to replace the metro’s outdated signaling system but the latest version involves more sweeping structural changes.
It is unclear how much revenue the tolls would bring in, but the non-profit Environmental Defense Fund estimates they would raise $1 billion a year.
“Since transportation makes up a third of New York’s greenhouse gas pollution, congestion pricing will help put the city and state on a trajectory to meet their ambitious climate goals” of reducing greenhouse gases by 80 percent by 2050, the Fund said in a statement.
The tolls would go into effect as soon as the electronic infrastructure is in place, no later than January 2020, according to the plan.
It also calls for reconfiguring the entrances to stations to prevent fare evasions.
The renovation plans will be reviewed by a group of independent experts, led by engineers from Cornell and Columbia universities.
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