At the Museum of  Science and Industry (several years ago) there were Nutrigrain bars and yogurt for DS.  However, when we are there, we are staying on 57th Street (same street as the museum) several blocks "inland". And where eat quite frequently is Medici on 57th. They handle food allergies well and they speak vegetarian fluently (thought there are carnivorous items as well.) I eat there when I go to Chicago twice a year. Because the functions I attend are weekend long meetings where everything's is catered, I often just get food at the Medici and take it back with me. I will say that I always lived their spinach pizza. It is the best!  But I have had reactions twice after eating it (mild) and have since learned an increment is XC with sesame. But I do okay with other things. I have trusted them enough with peanut to let DS walk and eat there by himself.

You didn't ask about the Field, but last time we were there they had a McDonald's.

There is a Qdoba doe the street west of the Millennium Park IC train stop (above ground). And there is a McD's in the theatre district.

Anyone visiting the Museum of Science and Industry or Brookfield Zoo in Chicago eat at the cafes there? Dealing with PA/TNA.