As far as I knew, you can't use the met card for ferry since the ferry is privately operated and you have to buy the ferry ticket separately. There is a ferry avilable between city and the Williamstown operating four times daily and it'll take an hour journey. You can explore the picturesque gardens and bay views during the trip.
Cruising in Australia is a great experience and no visit to Melbourne would be complete without Yarra River cruise. If you are interested then contact "melbcruises",one of the tour operators on 03 8610 2600 and book your cruise. Best wishes.