Last month, the MTA said the repairs would take at least a year.
But on Thursday, the agency said it estimates that fully restoring the station would take much longer and cost $600 million.
That includes $350 million for physical repairs; $200 million for signal replacement; $30 million for third-rail equipment and $20 million for line equipment.
The South Ferry subway station, at Manhattan's southern tip, was inundated with water up to its ceiling during the storm.
The No. 1 train station underwent a $545 million renovation and expansion in 2009.
The station is a major conduit to the Staten Island and Liberty Island ferries.
