Thanks for asking this Justin, it shows your commitment.
Knowing that Fedex is using Sagawa as their contractor in Japan, I wouldn't choose Fedex. Sagawa is the worse of all the japanese transportation companies, in Tokyo at least. They use a lot of temp staff, with larger delivery zones, and that leads to deliveries being delayed, or postponed. At best the quality of the service is highly varying depending on your location.
As stated earlier, EMS is cheaper, keeps the package at the post office if you're not home, and the customs' fees are reasonable. To me it's the best deal.
For other countries, the choice might be different, based on the delivery time. In Europe, for example, EMS can take a week to pass customs. However I bet that Fedex would charge you 3 or 4 times more to clear the customs in 2 or 3 days less. Problem is, the client is charged directly, so it can be a very unpleasant surprise when receiving the package.
Edited by frenchbat - 2/23/12 at 12:43am