What area will you be in?
Regardless,
Revolution and Half Acre both have excellent beer. Rev has a brewpub and HA has a tasting room. They both offer tours, but you'll have to get there early and stand in line for a while for those.
Goose Island Clyburn is pretty good and you can reserve a tour in advance.
Haymarket is always fun and also has a pretty good selection.
Piece is ok - I was just there Saturday and was underwelmed by both the beer and pizza. The first time I went it was pretty awesome from what I remember, so YMMV.
As far as bars, there's a huge selection. At the top of my list is the Map Room. Great selection, cash only.
Hop Leaf and Local Option are also great places to grab a bite and brew.
Maria's Packaged Goods is cool 'cause you can buy stuff to go.
As for bottle shops, most Binny's are great (South Loop will have the best selection, I believe) as well as West Lakeview Liquors. There's a new store I haven't made it to yet called The Beer Temple you might want to check out.
That's my short list,
here's the long list.
Enjoy!
