Don't know what to tell you about downtown Chicago rooms these days; even on average weekends the prices seem high to me. My family is paying $200 on an undistinguished summer weekend night this year.
Surely on marathon weekend everything in a nice hotel within 3 miles of the starting line has been or will be booked at a hefty rate.
Unglamorous surroundings in the MDW area, but close to an Orange Line station and maybe 20 minutes from downtown:
http://www.midwayhotelcenter.com/
I found availability 10/7-10/10, for example, at the Sleep Inn for $143.+ tax.
The Chicago Youth Hostel [(
www.chicagohostel.com) better than you might think] has bunk accommodations for $30 a person, segregated by gender. Call them to check on private rooms at about $100 rack rate.
I guess you could reserve somewhere with cancellation privileges and keep checking Hotwire/Priceline.
I fear the days of the $89 Palmer House room are gone for good. Bummer, my parents loved that.
I just checked Country Inn and Suites in Matteson, IL, about 30 minutes by car from downtown or 40 minutes by train a few miles away by cab and found a rate of $82 for those days. Not gorgeous, but something...
Maybe I should open a B&B.