The one tour I would skip is the Sitka boat excursion. While I love any boat ride, we didn't see much of anything. Eagles, yes, but got a much closer look just walking around. DH loved Tongas. He rented a bike on his own. I walked to the Russian Orthodox church, then browsed art in shops. Would do Raptor center if I ever get to go again.
Whale watching in Juneau was amazing! Humpbacks and orcas very near by. Lifetime memory stuff...ahhh.