I read close to 40 Alaska specific threads before going on our cruise last week, so my information is no means new (since our excursions were ones mentioned over and over), but it is current.
Skagway - We went with Chilkoot Tours. Our guide was Stanley, and she was fantastic. We trained up and bussed back. We add lunch at Carcross and the Dog Cart. We were in a van with 17 people total (we were a group of 10 to begin with). It was a bit of wait for Stanley because she was picking up a few people at the other dock, but nothing unbearable. We had our bug spray handy luckily. The dock was the worst for mosquitoes. Once we were all in the van, we headed to the train. We had to wait for all of the busses to get their passengers delivered and then we were off. As soon as the train rain was over, Stanley was ready for us. We started heading down the road and had a bear sighting. We quickly turned around, and after much searching found the bear. There were two coach busses behind us that according to Stanley were very happy we stopped because the big busses aren't allowed to stop on the road. There were many stops along the road where we got out of the shuttle, and took pictures and walked around. A great day!
Juneau - We went with Harv and Marv. We were on the Alaskan (which they call the Mercedes), and it was super comfortable. As mentioned before, we were a group of 10 so had our own boat. There was a naturalist as well as the captain on board. We were picked up at the dock, driven to where we would find the boat (with a nice talk about what we were seeing), and then off on our adventure. This was a rainy morning, but not too cold. As we were heading out to find whiles, ALL the boats headed to the right...but us. We went to the left and were completely alone until we found about 10 whales hanging out together. Once our captain radioed the other boats, we were no longer alone. We saw breaching, bubble netting, and everything else imaginable. There was even a calf who was having the best time playing in the water. What a successful trip! Then it was back to the van to visit Mendenhall Glacier. It was raining pretty good at this point, but our driver gave us some extra time to get pictures. He was supposed give us 15 minutes, but extended it to 30. Which was perfect due to the rain. If it was a nice day, I would have paid the extra money and taken the shuttle back to town and spent more time exploring, but alas that wasn't the case.
Ketchikan - We went with Island Wings. Again another great choice. We used two float planes - Michelle the owner of Island Wings contracted with another plane because she can only handle six for sight seeing. We were with her for two hours of beautiful flying. We landed on a lake, got out of the float plane and walked around, and then after about 15 minutes got back in the plane to fly back. What beautiful country!!! She narrated and answered questions the majority of the time. Simply awesome!!
Let me know if you have any questions!