You might want to stop by the Japanese market at Golf and Arlington Heights Road (Mitsuwa Marketplace). They have a JTB counter (Japanese travel agency) with particularly good rates. You often will get slightly cheaper rates out of Chicago on Northwest or even Delta (because you stop in Minneapolis or Detroit or Atlanta). Depends on what frequent flyer program you like.
If you're into frequent flyer miles, Northwest, Delta and Continental are all reasonably integrated, ANA and United/JAL and American also.
There are some slightly more exotic options as well (Korean through Seoul, Continental through Newark, Air Canada through Vancouver, United through Honolulu!), plus various connections (gateway cities to Japan are LA, SFO, Portland, Seattle, Dallas, Chicago, Minneapolis, Washington, Detroit, New York, Atlanta).
Also, when traveling overseas, you get 24 hours to connect at the gateway city (nice for a quick visit to, say, Seattle if you've never been there before). Finally, you frequently can have a free or very low cost several day stopover in that gateway city (even on the cheap tickets).
Your travel agent is a good investment for a trip like this to help you maximize the value of your trip
http://www.jtbusa.com/en/