Since only Japanese credit cards (one that require a Japanese mailing address) can be used on the Japanese PlayStation Store, the best method for funding a Japanese PlayStation Network account is to purchase Japanese PlayStation Network "gift" cards (also known as point cards.) They come in denominations of 1000円, 3000円, 5000円, and 10000円. The lower amounts tend to have a higher profit margin premium on them.
Re-sellers (especially ones not based in Japan and/or individuals) thus have to tack on their own margin when they purchase retail which can greatly increase the prices. Play-Asia is a reputable Hong Kong based reseller that sells these network cards but has a roughly 20-30% markup on them. They will e-mail out the code once your purchase has been billed. Another reliable reseller is cardcodes.com. Similarly, their markups are on the higher side.
Two Japan-based companies also sell these gift/point cards at what are the lowest prices in USD: Neowing's english arm, CD Japan as well as SolarisJapan.com (which also sells on eBay.) Both are reputable companies which I've also used without problems. Their markups are about the same; SolarisJapan however will e-mail your code quickly and also offers the ¥10000 card with just a 10% premium (which offers the best value.) At the current USD - ¥ exchange rate ($1 = ¥119.5979) for example, a ¥10000 card costs only $92. Most every other reseller is at least $10 higher.
Myself, I use SolarisJapan exclusively now once I use up the cards I purchased when I go back to Japan since I don't want to bother family/friends with my obsessions while I'm back in the US. I don't recommend Amazon Japan since most of the listings there are from resellers with extremely high markups and sketchy reputations.