I'd second the recommendation for Pike Brewing. I've always enjoyed it there.
If you get up north of downtown at all, I'd also recommend touring the Red Hook brewery in Woodinville.
I'm also a big fan of Naked City Brewing and Taphouse, at 8564 Greenwood Ave N, Seattle. Great food, nice people, and a constantly-rotating wall of the best craft beer around, including a few of their own creations. Also, they have an EXTENSIVE collection of bottled belgian beer. Naked City is always on my list when I go to Seattle.