And before you book any flights, make sure you have an eTA for all the members of the family. There are still people that are losing a lot of $$$ because it didn't come in time, or they were denied.
From Nanaimo to Tofino is a three hour drive, no stops. But there is plenty to see on the way to the west coast. Do have a look through the links above, and see what interests you and the family the most.
I'd want 3 nights in Tofino or Ucluelet for sure.
And yes, drop Whistler. Love that place, but I'd want to give more time to the Island. Depending on how much luggage you will be hauling around with you, you could walk on the ferry, and then pick up the rental car at Departure Bay, Nanaimo. Enterprise and Budget pick you up at the terminal, and take you to their office.
But check Canadian Affair for rental cars too. That would be easiest, as they have participating cities for rental cars, that don't charge the one way drop fee. Sometimes having a car is worth the extra expense.
If you do rent the car in Vancouver, avoid Budget, downtown location as well as the airport.
Also, if you rent the car in Vancouver to drive to Vancouver Island, you will absolutely want to reserve the ferry. You don't reserve for walk on passengers. When you make the reservation, you only pay the $10.00 reservation fee. The rest of the $$ is paid once you arrive at the ticket booth.