We go to the San Juan Islands in Washington every year, we finally ponied up the dollars for a whale watching trip. Unless you're lucky, have a fast boat, or both...this is the best way to go.
We went with Maya's Charters on San Juan island. Link here
http://www.mayaswhalewatch.biz/There are a many boats to choose from, we just like that with 6 of us, it was essentially a private charter for about the same price as a large tour boat.
We were lucky and saw Orcas, the tour before ours didn't see any, the tour after ours, two pods joined up and there were 60 plus whales. Just luck what you will see.
There were easily 20-30 boats following the pod...so I'd guess any tour would work. Boats out of Victoria, BC tended to be large inflatables, they looked fast and fun, but I doubt you would want your camera exposed.
I would recommend you take the whale watching trip early in case you don't see them on the first outing and want to go again.
Good luck - and I'd love to see anyone's tips or thoughts on getting decent shots, it is incredibly challenging. I used a 20D and 100-400, I would've given up the reach for the bigger viewfinder of the 5D, framing and staying on the whales was tough.
Cheers,
Scott