since bbentler posted this question in several forums, figured since this had the most hits I'd copy my response here.
My 4 favorite Chicago Stores. I get sale e-mails from the first 2, PM your email if you want and I'll forward them.
Old town Aquarium ~ One of the few stores in the city I regularly buy livestock from. They have the best livestock of any store and I (stupidly) don't even think about QT purchases from here. But they also are located in prime real estate downtown, so you pay prime prices, but there selection of plants and angels are pretty good, however its a small store and sometimes pickings can be slim depending on how busy they've been (think they get 2 shipments of fish and 2 shipments of plants weekly). Park in Pipers Alley on North Avenue and they will validate your parking with a $25 purchase, street parking is impossible there.
http://www.oldtownaquarium.com/
Living Sea Aquarium ~ In the northern 'burbs towards O'Hare, they also have a good selection of fish, but their plant section is slim if I remember correctly. I just found this place about 8 months ago, and usually just shop their SW section, so they might have more plants then I think.
http://www.livingseaaquarium.com/
Scott's Pet Shop ~ In western 'burbs off I-55, place is huge, and I'm surprised they don't have their own website. Lots of plants and FW selection. Don't think their plants were in A-1 condition like Old Town, but they have a large selection.
http://www.yelp.com/biz/scotts-pet-shop-westchester
Aquarium Adventures (Petland, Inc)~ Went to the Bolingbrook location during the grand opening last year and love this place. Its about the size of a large chain pet store, but 50% of the location is aquarium and pond fish and supplies. I bring my wife and son, they play with the dogs, cats, and birds (the employees encourage it), as I shop the fish (and try to pay while they are off on the other side of the store to avoid "money talks") The first time I was there I was shopping for koi angelfish and they had a sale on them, but the employee told me they had some kind of problem with those fish dying and advised against buying from that batch, so I give props for that.
http://www.aquariumadventure.com/