As you have noticed, most suburban Chicagoans will recommend against anything in the city LOL We try to avoid it at all costs!
I second doing stuff in the suburbs. Chicago Improv at Woodfield Mall is great,and I *think* there is a
LEGOLAND there, too. I highly suggest the Brookfield Zoo, but maybe because that is practically in our backyard (and literally right next to my kids' future high school) and we walk to it??!! LOL Going in the other direction, one of our family's most favorite thing to do on a weekend is go to Cantigny in Wheaton - it is absolutely amazing and is only a $5 donation per car. There is a LOT of new stuff to do near Ohare in Rosemont - The Big 10 offices/museum is there now if anyone is into college football, plus the fashion outlet mall, and I-Fly Indoor Skydiving (not sure when that is going to open though...DH passes it every day on the way to work and he says it doesn't look open yet).
Going downtown, I would say the MSI is really fun, probably my fave museum (Be aware, however, that it is not downtown - it is several miles south of downtown). I was so afraid you were going to say you wanted to got to the Aquarium and I was going to seriously have to tell you not to waste your money or 2 hours of your life waiting in a ridiculously long line waiting just to get in!!!
At the north end of Michigan Ave, you will find American Girl, which is across the street from the John Hancock. Cheesecake Factory is on the bottom floor of the JH. But it is super crowded all the time, and we actually prefer the CF in Oak Brook to the one downtown. In that area is also the water tower,
Disney Store, Garretts Popcorn (about 2 blocks south and around the corner....you cannot miss the smell of caramel corn!!!), Hershey store, Ghirardelli store, Nike store, etc. It's pretty walkable. We usually take the Metra Burlington from Brookfield to Union Station, then the Water Taxi to Michigan Ave. Then you just head north! It's about 5-6 blocks or so. Not a bad walk. If you wanted to go to Navy Pier, you could stay on the water taxi and head to Navy Pier. Kids under 10 love the Children's Museum, but really the rest of the Pier is pretty much a tourist trap. I mean, $30 for a family of 5 to go on a ferris wheel for only 1 full turn??!! Ripoff!!! We don't go up in any towers LOL...$100 bucks for our family to wait in a really long line to ride in an elevator to stand at the top of a really big building is not how we spend our money. Oh, and if you want to fit in here, please, please, please just call it the Sears Tower LOL
If you wanted to take a metra train to Union Station from wherever you are staying, you can go out of Union Station on the south side of the building and catch a bus that will take you to Grant Park, then transfer to the one that takes you to the MSI. It's really not hard to navigate, and the drivers are usually pretty nice about telling you where they are going and what bus you need. You can also map your travel plans on the CTA/Metra websites.
I do find it really weird that you would travel to Chicago, then stay about an hour outside of the city in Gurnee. As a matter of fact, DS13 just brought home his 8th grade Great America trip permission slip today, which is in Gurnee, and they are taking charter busses to Great America from Brookfield! LOL I think this is a *little* over the top....seriously, it's only about an hour's drive, do these little cupcakes REALLY need charter busses to travel on??!! LOL Oh, well...
Anyway, there are much nearer and WAYYYYYY more convenient suburbs to stay in. I suggest Downers Grove, Oak Brook, LaGrange, Brookfield area for ease of metra trains, or even Schaumburg or Rosemont because of all the great attractions that are so local and much easier (and cheaper) to get to.
As for food...of course you have to have pizza!!! Lou Malnetti's is gross (IMO!), but Gioradano's (stuffed with sausage, NOT thin crust here. There are way better places to get thin crust pizza in Chicago). I'd resist the urge to go to Geno's East or West or whatever it is near Michigan Ave....crazy busy and expensive for not as good pizza. I would also rethink Ed Debevics - you ca get a bad hamburger anywhere!! I would go to Cheesecake Factory - they have the BEST small plates. I don't think we have ever had a bad meal there, but again, we go to Oak Brook rather than downtown. In the MI Ave area, the Grand Luxe Café is also pretty good, or even the Walnut Room in Macy's (Marshall Fields to true Chicago Natives!)