About $535 million of the funding will go toward repairs of three tunnels under the river badly damaged in the Oct. 2012 storm — the Montague, Steinway and Greenpoint.
The closure will affect the R train, which carries tens of thousands of riders between Manhattan and southern Brooklyn. The work will likely begin in August and is expected to last 12 to 14 months.
After seven months of limited service and an estimated $650 million in hurricane damage, regular service on the A train is rolling through the Rockaways.
Federal money has been flowing into the New York Metro area to help transit agencies hit hard by Superstorm Sandy.
While Gov. Chris Christie justified his decision Thursday to scrap the state’s most ambitious public works project, the federal government is stepping in Friday to attempt and bring it back to life.