Depending on where you stay you should look at flights which originate from you home town. Especially if airlines give special deals and offers to fly to Japan.
Its cheaper to buy direct form airlines depending on their offers.
Should look at Ana offers and deals at
http://www.ana.co.jpYou can also try Zuji.com and or other travel/ticketing portals. Such portals get the same pricing as the public unless the portals have special deals. Usually such sites mark up a 50 to 100 dollars more