Thanks for all the recs guys. Here is brief trip report:
The W Lakeshore was nice. Not super luxe but the rooms are fine and the PH floor (not the top floor but 31st/33) has very nice views of lake and Navy Pier.
The weather was rainy (and cold) on July 1 so we went to the Art Institute in the afternoon. Very nice building and awesome collection of impressionist art and more contemporary works. We then wandered around the Taste of Chicago and ate some yummy fresh cut fried potato chips and other assorted street food + beer... I hate that they make you buy tickets for the food but I appreciate that they sell tasting portions so you can sample different things.
We headed back to the W to relax before dinner

. I really wanted to go to MK (the menu looked great) but it was closed for two weeks and Ricardo was a little out of the way; Blackbird's menu didn't do it for me for some reason. I wanted a steak and my wife was indifferent (and napped until 9pm) so we did end up going to Gibson's since we wanted to go to one of the Jazz bars nearby afterwards. The filet was nice. Peppercorn sauce was decent. Nothing too fancy but a good piece of meat with some nice wine. The stereotypical "viagra triangle" crowd was in full force at the bar. Makes for some interesting people watching.
The next morning we did the boat tour, which was excellent - smallish boat, very interesting and great guide (use Chicago Line tours).

We had lunch at Bin 36. The food was alright but nothing extraordinary. Their Pinot Noir was very good though. We then wandered along Michigan Ave. and bought stuff for the kids at the Lego Store (my son is very into Star Wars and they had some cool life size legos of Darth Vader, R2D2...) before heading out to O'hare at 7pm. We ate a sandwich at Berghoff Cafe there.
A thoroughly enjoyable, albeit short, visit. Chicago is a great city and while there are many similarities with Toronto, it's like a much better version of Toronto in many ways - particularly from an architectural pov. Thanks for all the tips!