The Map Room or The Hop Leaf have great selections but you might as well go straight to the breweries. Piece is a brewpub/pizza joint but they don't make Chicago style, for pizza try Lou Manati's, Stefano's, Gino's, or Giordano's in that order. I'd suggest going to Haymarket, Revolution, and Half Acre. HA has Saturday tours for $10, you get a mug and way too much beer, I've gotten pretty tipsy there off "samples" just make sure to be there early as there's always a line. Two Brothers is great if you want to travel to the burbs (Cane and Ebel rocks). I'm not sure if they're accessible by the metra? If you have a car and are adventurous 3 Floyd's is an hour to hour and a half from downtown and of course is amazing, though you would certainly be able to find their main beers at any respectable beer bar it would be lucky to stumble upon Zombie Dust or anything else more rare from them.
“… Besides, the Word is the principal part of baptism. If in an emergency there’s no water at hand, it doesn’t matter whether water or beer is used.” ~Martin Luther