The underwater tunnel was one of nine that was flooded during the October 2012 storm.
MTA Chief Tom Prendergast said work is ongoing at the Montague tunnel between Brooklyn and Manhattan on the R line. It is expected to reopen in October.
“Once we restore Montague, I think we’re down to South Ferry at that point and it’s the fortified part, the resiliency that we need to make sure we do,” Prendergast said. “It’s not a matter of if, it’s a matter of when the next hurricane is going to come.”