Do it after you touch down at NRT, using your ATM card to draw yen from an airport ATM such as the 7-11 ATM's in the arrival concourse area. You should probably have at least $100 cash on hand, just in case the ATM doesn't work for whatever reason and you have some emergency cash to exchange to yen.

It looks like ATM's in Jpn that take foreign cards do take pins that are more than 4 digits. But I wouldn't know personally. If you don't want to take any chances, change your pin to 4 digits.

Call your bank and make sure you're aware of any fees associated with using a foreign ATM machine. But assuming you have credit card with no foreign transaction fees, you can plan to use credit card for most of your spending. Places where you can't use credit card would include buying train tickets via machine, loading Suica/Pasmo card, some restaurants, some attractions, some independent stores.