Rainforest Cafe?!?!?! NOOOOOOOOOO!
It used to drive me crazy when my friends would come into town and want to eat at a chain restaurant. You're in a city with all kinds of AMAZING foods and you want something you can get anywhere?
Ok off my soapbox now
here's my recommendations:
Restaurants:
Bongo Room for breakfast.
Kuma's for burgers.
Hot Doug's for hot dogs.
Big Star for tacos.
Piece for pizza.
Portillos for fast food, get the chocolate cake.
Chop House or Gibson's for expensive steak dinner.
Those are my favorite places (besides Hot Dougs I've never been there, I just know it's good, be prepared to wait an hour or more at Kuma's or Hot Dougs) check out yelp to confirm my good taste
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I love the art institute, and Shedd and Field museum! You can't go wrong with any of those. For a zoo, I would go to Lincoln Park for convenience unless you are driving then I would pick Brookfield.
For drinks:
If you are into punk/rock music I love Delilah's on Lincoln
If you want to get all dolled up and go to some place unique I recommend the Violet Hour, an old speakeasy in Wicker Park (where Piece and Big Star are), it's pretty on the inside and the drinks are pretty freaking tasty! It has no signs or windows so it can be tricky to find, it has just a light on the outside of the building signaling if its open or not.
Instead of Willis Tower I recommend going to have a drink in the signature lounge in the Hancock building. You will have amazing views of the city (even in the ladies bathroom) and you get a drink for your "admission price".
There is a lot of fun things to do. I love Second City comedy club where a lot of famous people got their start. Chicago Food Planet has some fun awesome tours where you walk around a neighborhood in Chicago and you learn about the history of it and sample food at about 6 different restaurants! I've only been on the Wicker Park tour but it's so worth the $40 (yelp has a coupon to get 10% or 15% off). There's also haunted tours (fun!), and architectural tours by the river in a boat. Check out groupon for good deals.
I would skip Navy Pier for sure its beyond lame and not worth any of your time.
I could go on and on but I'll stop now. Have fun