I have been in Alaska and have watched whales in Zodiacs (rubber pontoon boats) - and the weather was beautiful. Of course, that is not a guarantee.
I am just saying that if the weather is very cold you might appreciate the glassed in boats, but i have been in the open to watch whales and it was just fine. For pictures & just in general I prefer no glass.
There was a very well-known tour company Dolphin Tours which picks up cruisers right at the port area in a bus and shuttles them to Auki Bay. Just as convenient as a ship's tour and much cheaper. As far as I know they are still there.