Last fall, I was able to get very nice rooms in the Marriott and in the Westin very near to the Navy Pier through Priceline for about $50 a night, staying on a Friday and Saturday night each time.
I'm bidding on an April trip right now, but haven't gotten an accepted offer for less than $60 yet, but it's almost 2 months before my next trip. Hopefully, as the date gets closer, I'll be able to get a good rate.
DH got a little ticked at me, but I googled a site (can't remember the URL, sorry) and found places to park cheaper than the hotel parking. We had to walk a couple blocks to the hotels, but we saved half the parking costs each stay. We rode the bus and El while we were there, and just left the car parked the entire trip, so we didn't need in/out privileges.
Here's a tip if you are going to be visiting mostly places on the CTA El and bus lines: Get a 1, 2, or 3 day unlimited pass before you go. At
http://www.transitchicago.com/ you can see their routes and order the passes, free shipping, or you can buy your passes at the Dominick's grocery store chain or at the Currency Exchange.
I like the Shedd, but I prefer the Field Museum or the Adler Planetarium.
Another tip to save is to see if you have a local museum that has reciprocal entry benefits through the ASTC program. I bought a membership to our local children's science museum even though I never go there now that my kids are grown. I wanted the membership just to go to museums elsewhere, and I have gotten my money's worth. Check at
http://www.astc.org/passport/ to see if you could join a museum near you.
Have fun. (We'll be back up there the weekend of April 9-11.)