If you want definite sightings of Orca, then Vancouver is probably the place to go. They have a resident population that's always around, and lots of boats spotting where they are each day and telling each other! Though as previously pointed out, that does mean there tends to be a lot of boats around when you actually get to see the whales, which perhaps detracts from the 'naturalness'.
A bit of fine tuning on that that I've learnt (at least this was the situation a few years ago...). The southern resident population ranges between Vancouver and the south end of Vancouver Island, near Victoria. They spend more time at the Victoria end. This means that going from Victoria you'll probably spend less time on the boat, but if the whales are actually up at the Vancouver end, they won't travel up there, and sightings are not guarenteed. If you take a tour from the Vancouver end (as I did) then they are more set up to do the long trip down south, as they did on the day I went. That means several hours on the boat before you see the whales. But the Vancouver operators tend to guarentee sightings, which means if you don't see a whale, you get a free trip another day.
Either way you get to spend 20 minutes or so tops around the whales (that's the regulations...). And of course trips can be cancelled due to bad weather.