A lot of it will depend on your interests. If wildlife is your focus, I might opt for the whale watching in Juneau, but if having a new experience is your preference, then either one will work. They all sound like good choices!
I did the whale watching in Juneau. We saw alot of whales and had Orcas come up and swim right along the excursion boat. I have a blue eyed Siberian Husky so I know how cute those dogs can be though!!
We chartered a boat in Juneau. We find it better to get a small boat, you can get closer. We us ak alasaka whale watching. In ketchican we did a float plane with seawind aviation. That was the best part of our trip.