I was thinking about heading to Vancouver/Victoria later this summer.  I know Canada is getting crazy with their laws and regulations, is anyone familiar with a tour operator that would allow using a drone to film whales (could be a tour or private charter, doesnt matter).

Not a chance without an SFOC permit which they probably wouldn't grant to you unless you were a movie company.  It's not up to the tour operator ... it's up to Transport Canada and they don't want anyone flying near buildings boats cars other planes people pretty much anything you can think of including animals.