We stayed at Embassy Suites by Hilton Downtown (River North) last year and Embassy Suites Chicago Downtown Magnificent Mile (Streeterville) this year. The first mile of the race runs right past where we stayed this year on Columbus. I'm not sure if I have a real preference between the 2 locations. This year's was probably a little closer to the start.
Hotel rates are high for this event, but I guess that's not a surprise to anyone. And parking is at a premium in Chicago. Also, some hotels will show no availability (if you try to book direct) because the organization blocks off a lot of rooms in the city but you can book through a link on the Chicago Marathon website. I didn't do this either year. Both years I booked through Hilton, but I was baffled this year when I couldn't find any availability at the River North ES 10 months in advance... I later realized it was because so many of the rooms downtown are held for the marathon. I never thought to go through the Chicago Marathon website to find my hotel. Once I decided I was going to apply to run, I quickly started looking for rooms because I wanted to be in a decent location (close enough to walk, near restaurants, etc).