For Juneau, one suggestion I have is to hike Mendenhall Glacier. You can get there quickly by public bus. Once there, there are a number of trails to choose from. I'm not quite sure how close you can actually get to the glacier, though, but information should be available on their Web site: http://www.fs.fed.us/r10/tongass/districts/mendenhall/
We are also cruising to Alaska soon, and booked a tour in Ketchikan through the cruise line that visits the Alaska Rain Forest Sanctuary. It's a short hike -- only a half-mile, I believe -- and it was actually less expensive to book through the cruise line than with the operator. Then again, you'd get more time there if you booked on your own.
I'm sure others will come along with more ideas. Happy planning!