I agree with Tom the Shee-Atika Lodge downtown is a nice place to sit and enjoy a seafood lunch. You can order one of Alaska Brewery beers there too. The Bayview Resturant on the second floor of the McDonald Trading Co. Building also has a good seafood lunch menu and your choice of alaska (and other) beers.
I recommend seeing the Rapter Center while you are visiting Sitka. This is a good spot to see various birds including the bald eagle up close.