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Mayor Bill de Blasio threw his support behind congestion pricing on Tuesday as the best option to raise money for New York City’s failing subway, announcing an unusual alliance with Gov. Andrew M. Cuomo, his frequent rival, to fix the system.

Their joining forces could give congestion pricing momentum as state lawmakers debate whether to embrace Mr. Cuomo’s proposal to toll cars entering the busiest parts of Manhattan. The idea has long faced difficult odds in Albany, and a proposal by former Mayor Michael R. Bloomberg was defeated a decade ago.

But with the subway in crisis and the streets of Manhattan choked by traffic, Mr. Cuomo has argued that the proposal is the best option for raising billions of dollars and reducing congestion. For months, Mr. de Blasio had resisted endorsing congestion pricing and instead favored a tax on wealthy New Yorkers.

With state lawmakers facing an April 1 deadline to consider congestion pricing as part of the budget, Mr. de Blasio decided to back the idea to help mitigate the region’s transportation crisis.