I first did this in 2008 and it needs to be updated. For one thing, the number of Chicago bars with a fulsome selection of American whiskeys has exploded in the last few years.
The best place to buy bourbon and rye by the bottle is still Binny's. I'm sure many people wish it could be some little boutique in a funky neighborhood, but it isn't. They simply have everything. As their slogan goes, if you can't find it at Binny's, it probably isn't worth drinking. Or it's universally sold out.
Not all Binny's are created equal, however. I haven't shopped all 29 locations, but of the ones I know, South Loop on Jefferson just north of Roosevelt is the best. South Loop also has the advantage of being across the street from Manny's Deli, purveyors of the world's best pastrami and corned beef. (Tip: know what you want before you get in line.)
If you insist on someplace small and neighborhoody, Lush is a good choice. They have three locations, all in the city. Also good is In Fine Spirits, in Andersonville, especially if you want to try some locally-made products.
As for bars, there are too many to list. One of my new favorites is Longman & Eagle (2657 North Kedzie), in Logan Square, which is also a great restaurant. They even have a couple of rooms to rent where you can literally make a night of it.
Downtown the Berghoff Bar, at 17 W. Adams, has a limited bourbon selection but some of my favorites, not the least of which is their own private bottling, a Van Winkle wheater. The bar is beautiful. It has been called, "perhaps what the bar in heaven looks like." The restaurant proper closed in 2006 but the bar is still open, serving German food as well as drinks.
For many years, before the American whiskey renaissance, the Berghoff was Julian Van Winkle's biggest customer, so in a way you can thank (or blame) them for today's Pappy Van Winkle phenomenon.
In the Loop, I also like Miller's Pub (134 S. Wabash Street) for many of the same reasons. The bourbon selection is only so-so, but it's a real bar (also a pretty good restaurant), little changed in 50 years, cheap for a downtown joint, with convivial and professional drink slingers. It's civilized without being pretentious. For easy reference, it's a few steps south of the Wabash Street entrance to the Palmer House. Drinking on Wabash, under the L track, is itself a unique Chicago experience.
Both places allow you to imagine you're drinking in Chicago in the 1940s or, for that matter, the 1920s. Chicago was pretty much wide open throughout Prohibition. No sneaky speakeasies for Al Capone's town.
Outside the Loop, in the River North area, I'm fond of the Clark Street Ale House (742 N. Clark Street), which has a good selection of beer and whiskey, nice atmosphere, and is easy walking distance to some good blues bars, restaurants, and convenient public transportation. It's an easy way to get a little bit out of the Loop and Michigan Avenue neighborhoods where most visitors stay.
It also has the best sign ever (above).
Not too far from Clark Street is Sable (505 N State). It's a bit more dress-to-impress than any other bar on this list and although it tends toward cocktails, all of the bartenders are masters of straight spirits too. The kitchen is also of a very high order, and you can eat at the bar.
Rocks is good if you're looking for neighborhood atmosphere, acceptable pub grub, and a good whiskey selection with bartenders who know what's what. They have locations in Lakeview (3463 N Broadway) and Lincoln Park (1301 W Schubert). Good for the same reasons are Bar on Buena (910 W Buena) and Fountainhead (1970 W Montrose). Fountainhead has an elevated food offering too.
Far and away the best bourbon selection in town is at an unexpected place called Delilah’s (2771 N. Lincoln). If you imagine a bourbon bar as looking like an English men’s club, prepare for a shock. Delilah’s is more of a punk rock joint, but they have probably twice as many bourbons on offer as anyone else in town. Any lover of fine drink and serious rock and roll is always welcome but it gets too loud for conversation as the night wears on.
Delilah's doesn't serve food, but there's a Gino's East pizza right across the street.