That's plenty of time to do the brewery. Just make sure you have a cab lined up to get back; it isn't walking distance from JNU (nor is the brewery really near anything, unless you want to check out the Juneau Costco).

Also, the tour isn't really a tour. They have a big room where everybody sits down, and they tell the story of the brewery's history while giving you free beer.

Edit: Just an FYI, JNU does have precheck lite (keep your shoes on), but there isn't a separate line for elite passengers. So be prepared to stand with everyone else, although it usually moves pretty quickly.