I really want to echo the suggestion for Clark St. Ale House -- very solid beer list and a great selection of whiskies, too, along with a very comfortable back patio (which is finally useable!). It's also located close to the area you'll be staying in.
Juicy Wine Co. is also great for wine and cured meats and is pretty close to downtown, as well.
As others have said, there aren't a lot of local brewpubs. Goose Island is your best bet -- something in the order or 12 taps every day, only half of which ever get bottled.
Piece is another solid option, I'd say, if you like pizza with your beer. Piece is located steps from a blue line stop. Note that it's New Haven style pizza, so you can't get a Chicago-style fix while you're there. It's not earth-movingly amazing, but I like it just fine and their beer list is very respectable (they don't bottle beer for retail). They can also get pretty hectic if there's a game going on, but that can be part of the charm, too.
Three Floyds is amazing, but may not be worth it if your time is limited (it's about 30-45 minute drive from downtown). Any of the bars already mentioned will have some of their beer on tap, anyway (though there are usually 2-3 beers that are brewpub-only).
I wouldn't bother trying to head out to the Two Brothers brewpub, though. I've found the food to be completely 'meh' and their brewpub selection is no different than what you can get elsewhere in the city.
Lastly, I can't believe no one mentioned The Violet Hour yet! All you need to know about them can be found in
this thread.
Piece
http://www.piecechicago.com/flash/index.html1927 W. North Ave.
Chicago, IL
773.772.4422
The Violet Hour
http://www.theviolethour.com/1520 N. Damen Avenue
Chicago, IL
773.770.0184
best,
dan