A.R.
Hi! Well first off, I think you should just stick around in Naperville for the hotel prices and proximity to your doctor for certain. If you do take your son to Willis Tower, take a Metra train if you can. I have attached some links for you. The first is a list of Naperville eateries with gluten free. The second is information on the Skydeck at Willis Tower. (It kills me not to say Sears Tower, being a lifelong Chicagoan!) and the third link is for our transit train, the Metra. It’s safe, clean and affordable, and it let’s off just down the street from the tower.
http://www.urbanspoon.com/tn/2/1/12205/Chicago/Gluten-Fre...
http://metrarail.com/content/metra/en/home/maps_schedules...
I hope this is helpful!
Have fun in Chicago.
Xoxo