I've done the walking tour. Head to Brooklyn Brewery, then hit up Mugs Alehouse, then Spuyten Duyvil, then Barcade. If you cannot find good craft bars in Brooklyn, you aren't trying hard enough.
Many options. If near Park Slope, try Owl Farm and Bierkraft (not really a bar-bar, but it's a good choice).
What neighborhood will you be in? Brooklyn is very large and spread out. Some of my favorite (organized by neighborhood)... Williamsburg/Greenpoint: -Barcade -Spuyten Duyvil -Torst -Mugs Ale House -Brouwerij Lane -Dirck the Norseman -Brooklyn Brewery -d.b.a Brooklyn Park Slope: -Mission Dolores -Double Windsor -The Gate -Owl Farm -Bierkraft
Lucky Dog Mugs Ale House Brooklyn Tap House Brouwerij Lane Breukelen Bier Merchants Spuyten Duyvil Barcade