I just returned from Tokyo last week and found the ATM rates to be very competitive with the fx rates at the airport.
I have to admit that the fx window at Narita had very good rates, esp when compared with the rates at such windows in the US (terrible).
I highly recommend using the 7 Bank ATM's when arriving at Narita if you have a Visa debit card. No upfront fee, just whatever fee your local bank charges for using a foreign atm. Mine charged $1.50 transaction.
7 Bank is the 7/11 bank in Japan. You can find and use their ATM's in the many 7/11's in Japan with no upfront fee for Visa (there is a charge for MC debit users though).
jb