CAF's ArchiCenter is a great first stop for orienting oneself with its scale model of downtown, displays about the history and evolution of local architecture, a brochure with a map of notable buildings (not sure if that's online), tour catalog (buildings which get their own tours are all quite notable), and obviously tours -- which I highly recommend. They also have an on-site bookstore, of course. The "core" tours for beginners (offered several times daily) are the River Cruise, Historic Skyscrapers, and Modern Skyscrapers, but I think there are about 100 others on offer on a rotating basis; no other American city has such a resource.

For books, I trust the AIA Guide to Chicago (2nd edition), but it's kind of hefty -- and deservedly so. It was effectively my tour guide to the city for several years. There's a whole lot to see here...