The A, C and F trains will be shut down between Manhattan and Brooklyn in the future, the MTA said.
The MTA said it will increase fares in 2015 and 2017 by 4 percent, not the projected 7 percent.
The passageway will link the World Trade Center with Brookfield Place in Battery Park City.
A traffic group led by Sam Schwartz wants to add East River tolls, but lower toll prices citywide.
Single rides will cost straphangers $2.50 and weekly MetroCards will cost $112 come March.
Most of the FDR Drive was also closed Monday because of the storm.
Low-lying areas including Red Hook, Battery Park, and Far Rockaway, were flooded Monday.
Tunnel boring has been completed on three MTA megaprojects.
The tunnels are being lined with inch-thick plates and will have flood-gates at either end, according to the Post.
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