I assume you are looking for private tours?
Juneau: We did a combo whale watching and Mendenhall Glacier tour. Called Mendenhall Glacier & Juneau Whale Watching Combo Tour, it was through Juneau Whale Watch. We first did the whale watching, and then they had shuttle buses which took you to Mendenhall Glaicer. The nice thing was they run the big shuttle buses, and they run every 30 minutes, so you could stay as long as you wanted and just take a shutltle back when you were done. We hiked around a little bit, but as it began to rain, we ended a little earlier than planned.
Ketchikan: No tour here. We walked around town and ended up buying tickets to the Lumberjack show. We really enjoyed it. Again, it rained a lot, but we didn't care.
Skagway: So many people take the train. We did not, because I knew I wouldn't enjoy being on the track so near the edge and my girlfriend has back problems, and we didn't think she would like the train benches. We booked Dyea Dave and took the van both ways. 100% recommended. Wait, no, 150% recommended. Our guide was outstanding.Our guide wasn't local, but works winter in CO (ski slopes) and summers in Alaska, so quite experienced. She could spot a bear on the side of the road when we totally missed it and would turn that van around or back it up, so we'd get a great look.