We did those ports last year. In Skagway we did the haynes wilderness kayak trip. It was awsome. The lake we went to was up in the mountains.
In Ketchikan we did an air tour. We booked with Seawind aviation. They were the best part of our trip. The ship was late getting into port. The waited for us for a while, then arranged a later flight. The scenery in alaska is great, but from the air it was amazing. We were able to see bears, whales and at one point landed on a lake in the mountains. It is a little more than you want to spend, but worth it.
In Juneau we booked with AK alaska. The boat was smaller and there were just 4 of us on board. the small boat seemed to be able to get closer to the whales. I would look for smaller boats. If you would like to see pictures, e-mail me at firstname.lastname@example.org