J., you LIVE in Chicago!!! C'mon, girl, your niece is not going to be bored going to places she's never seen! Why not take the whole group and hang out at Navy Pier? There's enough to do there to keep everyone entertained, and you might even go there on more than one occasion.
I think Shedd Aquarium would be good as would the Adler Planetarium, Museum of Science and Industry, Field Museum, the Art Institute, and Brookfield. You might want to ask your niece which of these she'd most like to see, and go from there. How about taking them around Lincoln Park? A game at Wrigley Field? Sears tower? (I refuse to use the new name). ETA: Run around Millennium Park on a sunny day!
As far as the kids' sleeping arrangements, just tell your 11 what the plan is and don't indulge complaining about sharing with her siblings during the visit. If you expect her to complain, she'll meet your expectations. If you expect her to be flexible, she'll eventually follow suit because there's no other option. There's no need to give in to grumbling.
Why not give your niece another chance to have a big sleepover in the same room with her cousins? Just because it didn't work out before doesn't mean it can't now. Could be great fun for them and a way to make special memories. Use sleeping bags or just throw blankets and pillows on the floor or air mattresses. Kids love that!
I know this may go against your sensibilities, but to save yourself from being in the kitchen and doing tons of dishes, consider some disposable plates and cups, especially on days when you need to get out the door and on to your next adventure.
Have different drink options for them--- juices, teas, flavored or plain waters. If you can have their favorite shampoos, bath products, toiletries, and a hair dryer ready for them, then they won't have to pack those things.
Make sure to have extra toilet paper, kleenex, and laundry soap on hand so you don't have to run to the store for those things that will surely be used most. Three extra people in the house can make a big difference with these things!
Enjoy your visit!
J. F.