The only idea I had was Navy Peer.
Skip that - unless you like insane crowds and high prices for trinkets. It's kinda like Mackinac Island, or Brown County Indiana - only worse. If during the summer it is a good spot to go on Saturday nights for the (albeit brief) fireworks display. There is usually a decent band on stage in the Beer Garden all the way at the end of the pier. I would also recommend doing a lunch cruise from one of the many cruise liners along the pier. It is a bit pricey, but it is a couple hours away from crowds with a unique view of the city.
Check out the Field Museum, Science and Industry Museum, Shed Aquarium. Go see Blue Man Group, go to the top of Willis Tower
Skip this too - unless you are intending on going on a museum & history tour. Long lines to get in, over-crowded once inside, absolutely no place to sit down and take a load off and way over-priced. Plus you are stuck inside for hours while a beautiful city awaits outside.
Grey Line double decker bus tour was very informative, we really liked it.
This is a great idea, as is a boat-based architectural tour. Nice and relaxing, great views and informative. A walking tour along Michigan Ave, North Beach and also the northern shore of the Chicago River from Michigan Ave are enjoyable. Combine the last with a walk along Wacker Drive to the west from Michigan Ave.
Other ideas - go to the Signature Room Lounge (different from Signature Room Restaurant) in the Hancock Tower - go a couple hours before sunset and try to get a table on the glass to the west or the south, stay through the sunset and watch the lights come up in the city. They have food and drinks - but they are chicago priced. I'd also recommend a walking tour along the lakefront heading south from Wacker & the Chicago Yacht Club towards Soldier Field & the museum campus. Once near there you can cross Lake Shore Drive into Grant Park and check out Buckingham Fountain and The Bean, then walk north along S. Michigan Ave back towards the river.
In general - I recommend staying outdoors more than in... the charm of the city is in the views of it.... not necessarily being IN it.
If you want a motorcycle tour via Goldwing I am happy to oblige - but can only take 1 person at a time