This port is completely dependent on the weather. There is absolutely nothing to do in the city except for a hammer museum. That is a museum of hammers, by the way. We had a very nice time hiking and getting away from the ship, however. Apparently the ship goes back and forth between at Skagway and Haines and many people ferried to Skagway.
To be fair, most of what we wanted to do here was outdoorsy and the weather was awful. Because of this we ended up staying in town, which is very touristy and inauthentic. We did go the Alaskan Beer Brewery and enjoyed that tour. The advice given to us by the cruise ship's port planner sums Juneau up quite well: When we asked what one thing in Juneau was not to be missed, he thought about it and replied, "Well, if you had three days, I'd tell you to rent a car and get out of Juneau and go camping somewhere or something."
Ketchikan Outdoors is amazing! We got there and they had sold out of their first tour time but the owner called her husband and opened up another time for us. It ended up being just the two of us on the boat with our guide leading us in a separate boat. He was incredibly knowledgeable and interesting and catered the tour to our interests. We saw lots of wildlife, including a bear, sea lions, seals, and eagles. This was definitely the highlight of our trip! The town of Ketchikan is small but there is much more to it than Haines and it is not Disneyland Alaska like Juneau. Also Creek Street is great!