The ferry runs from Rockaway to Wall Street with a stop at Sunset Park, The Sunset park stop in 58th Street and 1st Avenue behind the old Army Terminal. I remember that area very well. I took a ship from there to go to Germany when I got drafted. Also returned there. Very different now.
It's a big pier with plenty of free parking. The ferry is $2.75 each way. and takes about 15 minutes. It's 45 minutes from Rockway making the trip from Rockaway to Wall street about an hour. There are reduced fares, just like MTA, for seniors and disabled. There is an application that needs to be printed and filled out for that but it looks like it's only for 30-day passes.
Check out their website for more information.