Ketchikan - I've always enjoyed the Lumberjack show and a side-trip out to Saxman Villiage. Both are inexpensive excursions and will allow plenty of time to explore town. Be sure to check out Ray Troll's shop, the Soho Coho on creek street... great local artist. IMO, Misty Fjords needs to be flown... such a huge area, that you really miss much of the splendor from a boat.
Juneau - The Tracy Arm trips are great. Adventure Bound and Alaskan Marine Adventures are the two regular Tracy Arm running tour boats. Price and schedule will vary between the two, as Alaskan Marine Adventures is a 6-pack boat, while Adventure bound runs 2 large vessels carrying between 12 and 50 per tour. One will customize your tour and one leaves the dock promptly every day, so if your port times don't match up, you're SOL...
Skagway - This is my favorite candidate for exploring without any excursions, although I still ride the WP&YR train for a short tour every time I'm there. Stop by the Forest Service, they've got a great walking tour and history lesson for Skagway, and don't forget to have a drink in the Red Onion Saloon...
Sitka - This is the port you want to go fishing at. Every chance I get, I drag the family out to the coast to have fun pulling on all sorts of fish... giant Pacific Halibut, King Salmon, rock-fish too various to list. Be sure to ask if anyone specializes in catching Sablefish as well... not many do, as they live in 1500'+...
Of the 4 ports, Juneau seems to have the best built infrastructure for moving folks around and the most variety of tours and excursions. We could probably fill a week or more just taking side-trips form Juneau. Ketchikan is good for about 2 days, 2 or 3 in Sitka, and Skagway is always a 1-day affair for me...not that you have that much time, just putting it into perspective.
Happy Alaska Travels!
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