I will be flying from Cedar Rapids to New York via Chicago and I want to visit Chicago. I searched and found that I can get 9 hours transit by having multiple tickets i.e. CID to ORD then ORD to NYC (since single ticket is offering up to 50 mins transit only). By doing so, I am going to land Chicago at 1300 hrs and fly at 2140 hrs for New York. I assume that I will get my checked baggage also which I can't afford to carry it to down town. what should I do with my checked baggage, is there any facility to deposit your checked baggage at O'Hare?
As of March 2016, you can't store your luggage at O'Hare:
Can I store luggage at the airport?
Currently there are no facilities or provision for the storage of luggage at O'Hare International Airport.
Your best bet (as noted by @MichaelHampton in the comments) is probably to give it to the airline for your ORD-NYC flight, and then leave the airport to do your sight-seeing.
You didn't ask but I'm telling you anyways: Your best bet is to take the CTA Blue Line to & from downtown. Allow 1 hour each way. Assuming that you want to get back to the airport by about 20:00, and that you won't actually be free of the airport until 14:30 (allowing for travel delays and the time to claim & re-check your bags), you still should have a good 3.5 hours in the downtown area. If it's a nice day, and you have some money to spare, I highly recommend a boat tour from the Chicago Architecture Foundation.