Cruise stops - need touristless restaurants [Juneau / Skagway ]
Oh jeepers wish Id seen this sooner but I've been doing a bit of my own traveling. In the event you haven't cruised yet, Juneau I can help you with....
Downtown will be busy with tourists regardless but there are places you can find that will not be too bad.
The Hangar on the Wharf will likely have a lot of tourists tho the downtown workers are in there pretty thick at lunch time. However, you can get some excellent bits from their menu at their outdoor stand the Flight Deck.
There are several food stands right next to the parking garage off the dock - Tracys crab shack is expensive from our perspective but the crab is well worth it. The crepe place there is pretty good too. These are outdoor spots so best enjoyed on a nice day.
There are other places that tourist don't usually frequent but aren't really the kind of "alaskan food" I would think you are looking for but here's a list:
El Sombrero - darn fine mexican from a local family who are all involved in the business
Kenny's Wok and Teriyaki - its the sushi bar that does it
Pizzeria Roma - great pie
Head over to Douglas to the Douglas Cafe for great burgers, sandwiches and different dinner fare than you might find other places or to the Island Pub for wood fired pizzas, sandwiches, salads.
1102 2nd St, Douglas, AK 99824
2 Marine Way Ste 104, Juneau, AK 99801