Don't take the "L", I tried that once and thought I would be killed by some of the less savory people of the southside. If you are staying at the Palmer house then walk to the South shore(Metra) RR station( about 10 minute walk) and take that the to the stop for the Museum.
http://www.metrarail.com/Sched/me/55th.shtml
There is also a nice pre-owned book store in the area of the above station. I think it is called Powell's
http://www.chicagotraveler.com/attra...-industry.html