Steve,
For info on Juneau trips try
http://www.goldbelttours.com/ They operate the tram, cruises, shops etc. Tram is a great trip, you can take it up and walk down if you want some exercise. Best part of Goldbelt is that they are the local Native Owned organization so you tend to get a much more "local" experience and your money goes right back into that community.
For Sitka, my suggestions would be the following:
From the ship, head towards Sheldon Jackson College- Built in the 1800 to educate Native Alaskans. One of the best Native Alaskan Museums west of D.C. ($4.00 per person) Michner lived here while writing his book on Alaska. There is also a decent (for Alaska) aquarium/hatchery there. This will take you 10 to 15 minutes to walk to, maybe a half hour to hour to tour. From here continue walking (maybe 5 minutes) to Sitka National Park
Sitka National Park- This includes a walk around Totem Park (free) and entrance into the cultural center ($8 per person)
www.nps.gov/sitk/ This should take an hour or so. Great place for photos, of the park and of your ship which will be anchored out in front of the park. Once you are finished, head through the park to the Raptor Center
Raptor Center
http://www.alaskaraptor.org/ Great place to see Eagles, the show takes half an hour and if you get front row seats you be roughly 5 feet or less from a live one. Beaks look larger and sharper that close. If the movie "Birds" scares you, SIT IT BACK! Walk around the center after the show takes 15 minutes. Carefull out back, brown bears sometimes hang out there. Try not to smell like smoke salmon. From Raptor Center, walk back through park to town. It's lunch time.
Lunch - BAYSIDE! Second floor, you can sit almost over the road and look out at Crescent Harbor and the bay beyond. Lunch probably $8 to $12 plus drinks (pricey for soft drinks and soda, but their milkshakes are worth the $4.00) Bayside is on the way back into town above the first jewelry store from the National Park. You can try the Westmark, but order from their bar menu or you'll pay through the nose. Ludvigs is also a great place, but small and hard to get into. Subway is cheap and usually there are a few hotdog stands if you want somewhat cheap street food (Reindeer Dogs!) There is also a great Sushi place in the middle of town, the cooks are two funny guys.
If you're stuffed from Bayview, walk the docks across the street. You can get onto all of Sitka's public docks, no keys no gates. Cresent has a good mix of commercial, charter and private. Chivita's usually down at the end by the tennis courts, also two or three other C-Dorys.
Downtown next! Sitka has by far the largest collection of "real" Alaskan artifacts. Sitka's in the middle of a pretty serious battle to keep Sitka unique, there are a few stores selling cheap asian crud, but most of what you will find is made by locals or Alaskans and it's sold by locals. There are a few jewelry stores, the one under Bayside is locally owned and operated and the owner (Chris) bets anyone who purchases from his store in December what the total rain for December will be. If the town wins, he refunds EVERY purchase for that month. Town won this past December to the tune of $150,000 plus! They don't come better than Chris!
If you want real local artwork, try the new shop downtown under Alaska Pacific Bank. Will cost a bit more but it is all local made by local natives.
If you want to witness some Native dances, try the Sheet'ka Kwaan Naa Kahidi Community House. They usually hav a show at 1 or so. The people that perform these dances are brought all over the world to perform. They are worth the time if you have it. The Naa Kahidi house is beautiful and it is Sitka's year around activity center. Very close to what you would have seen 200 years ago.
This should take you till probably three or so. Feel free to stop by the hotel if you still have some energy and want more ideas. I'm across from the Naa Kahidi and usually running around.
Yell if you want more info, I have to go as someone just brought some fresh smoked white king to the desk and if I don't get up there it will be gone!