Skip the chain restaurants. Obviously inland cities are not going to have as good of seafood as coastal cities but Boise has some really good local restaurants with fish and I have been told by friends in the business that the seafood is shipped fresh from Seattle a few times a week.
zoso1979 gave a few great ideas, Cottonwood Grill is delicious.
Chandlers has great seafood, kind of spendy.
Angells downtown in the bottom of the Simplot Headquarters building is nice, here is their menu.
Boise Steaks | Seafood Restaurant @ Angell's Bar and Grill
Berryhill in downtown is a fine restaurant with seafood on the menu
Berryhill & Co. - Menus (http://www.berryhillandco.com/menus - broken link)
Cafe Vicino is one of the best restaurants I have been to, anywhere.
Cafe Vicino
Basically, most of the more fine dining restaurants in the downtown area have a mix of seafood and steak, and other meats on their menus and downtown makes for more of a romantic evening than a strip mall or chain restaurant by Edwards Cinemas or Boise Towne Square.
Fresh Off The Hook near the mall is good as well.
If you like it raw there are a lot of sushi restaurants in downtown and around the city. Just Google for menus for the restaurants I did not post links for.
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