for the 210 & 250 routes, the ferry is included in part of the whole "round trip" around the bay, and the cost is included in your ticket. they have a couple of ferries running back and forth from queenscliff to sorrento, and you just line up and take the next available one.
however, if you are thinking of starting from sorrento and doing the 100km ride to melb the travel arrangements you make to get to the start are under your own steam. BV organises a bus to take people down (the cost is addition to the ride entry), or some people prefer to get to sorrento the day before and spend the night there (accom books quickly). so i imagine if you want to catch the ferry to sorrento on the morning of the ride, you would be best to contact the ferry company. they may not have ferries starting as early as you need to make it to the start in time, or all of their ferries might be "booked out" on the day to cater for the riders.
sorry, i dont know the name of the ferry company, perhaps the white pages can help you there depending on where you want to leave from (are you thinking of going to queenscliff, catching the ferry from there to sorrento and being at the start before ~8am?).
alternatively, if you already know you can ride 100kms, why dont you consider 200 or 210km?