My experience is the best possible rate is in Japan, rather than the US; with a better rate on cash, but only by a few percent. There's quick and efficient exchange at the airport and probably the only place you could get a better rate is a US base, but you need to be military for that. One point of etiquette: don't bother counting your exchanged currency. They're not going to cheat you and the Japanese never do. I guess though by now they expect it out of gaijin. The point about the best possible rate being credit card is true, since the major agencies use something close to the actual rate. However, there are, as mentioned limited opportunities to use them, as everybody carries around massive amounts of cash. One last point: you could just change fifty bucks or so at the airport, and then locate an ATM machine and get the same good rate (though of course there are fees with that too...). There's a CITIBANK in the Shibuya district of Tokyo; and ATM machines that accept foreign (in both senses of the word) cards under the tower in Kyoto.
You sure are travelling at the right time, aren't you, 125 Y = 1 USD !!! Happy travels... wish I could come along.