Food is pretty lackluster on Navy Pier, and healthy options in particular are few and far between.
Generally speaking, the restaurants can be divided into three categories: sit-down restaurants, mostly located in or near the family pavilion (the large open area that the museum is in), the food court (a couple of restaurants close to a large seating area in the family pavilion—McDonald's is the most prominent), and the smaller counter service restaurants along the long corridors of Navy Pier, with open seating across the hallway. It is usually very difficult to find highchairs along the open seating inlong corridor, and I'm not aware of any booster seats available for those.
If you're bringing your own food, you can usually find a table to sit at along the long corridor by the counter-service restaurants (turn right out of the children's museum and follow the path around a few corners until you get to a long hallway with windows and seating along the right side). Bringing your own food to the food court by McDonald's is not allowed, and you may be asked to move if you try, especially on busy days.
If there's any kind of crowd, I strongly encourage getting an early start to lunch (I always try to be at a restaurant at 11:30 to beat the rush).
See the More Information section to get more details on specific restaurants.
I also like Jimmy Buffett's Margaritaville. The kids menu includes a cheeseburger, chicken bites, mac and cheese, or even a half rack of ribs. Their salads are pretty good for adults, and they have good burgers as well.
Giordano's is a great choice, especially for out-of-town visitors wanting to experience Chicago-style pizza. Be aware that pizza, especially Chicago-style pizza, can take a while to prepare, so it's not a good choice for active or hungry kids. Chicago-style pizza can be pretty difficult for young kids (thick and very gooey/cheesy makes it easy to choke on a little), but Giordano's does have regular pizza as part of the kids menu.
I do not recommend Bubba Gump Shrimp Co. I've tried it a few times, and neither the kids nor my meals have ever been very good.
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