My first thought is to question whether you need a car for Whistler. Whistler is pretty self-contained and well served by public transport from Vancouver. You also don't say how long you are staying in Vancouver, or if you are just passing through the airport.
Second, let me comment on Victoria: Hotels a little out of town are not going to charge you for parking. Those in the centre probably will. Be aware that public transport from Victoria ferry to downtown Victoria is not cheap - depending on the car you want and the number of people, and how long you are staying in Victoria you might save money with a car.
I actually did your itinerary last year, without Whistler, and we opted for a one-way rental from Victoria to Nanaimo. We flew into Victoria and took the ferry out to Vancouver. It ended up being pretty reasonable, and easy enough to organize. (Though none of the car rentals are right by the ferry, so you will need a taxi - add enough time for this).
If you wanted to save the one-way rental I would pick the car up and drop off in Nanaimo (obviously taking the ferry to Nanaimo both ways). Victoria is only a couple of hours by highway, and you would avoid the drive from downtown Victoria to the ferry.
I would price out both the following options and see which works best for you:
- One way rental from Victoria to Nanaimo, adding in the cost of public transport from the ferry to Victoria.
- Rental for the whole period starting and ending in Nanaimo, and including parking if your hotel doesn't provide it free.
What car you want and if you need insurance might make the difference in which is cheaper.