Hi SamC,
Welcome to the forum. I'm from Germany too, but have been living in Canada for a few years now.
If you want to do whale watching from Vancouver, Google whale watching Vancouver and it should give you a few options. I think most of those tours are day trips, because it takes a a while just to get out there. You'll probably have to go downtown though to catch a ship.
You can travel to Vancouver Island by plane or ferry/bus. I did the ferry/bus on a September weekend once and unfortunately the bus trip wasn't the best. bus was packed!!! It is cheaper than flying though, unless you get a good rate with Westjet or Air Canada. (or you could take a sea plane)
I did the Alaska cruise a few years ago (also in September) and i really enjoyed it. I'm planning on doing it again this year, but have nothing booked yet.
Listen to me going on and on. That was the travel agent in me talking

Would love to meet you and everybody else of course. I will be in seat O19.
Heike