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!
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.