Amazon.co.jp is definitely the most convenient since they handle the shipping and accept foreign payments. Shipping is very reasonable IMO.
However, sometimes the prices on Amazon.co.jp are not the best and don't have more unusual unique tools. Using a Japanese domestic e-commerce site like Rakuten is your best bet but you'll need a domestic address in Japan to ship to and have a credit card that can accepted Japanese Yen (ideally with no foreign FX fee).
Here's a Japanese Rakuten store that I've used that has a great selection of tools, including wonderful photos:
エヒメマシンは京都機械工具(KTC)特約店・TONE特約店・ボッシュパートナークラブ契約店です。その他にもコーケン・シナノ・ハスコ・長崎ジャッキ・マサダ製作所・ミズノ・ジェントス・レッドレンザーなど様々なメーカー工具・LEDライト・グッズを正規店として取り扱っています。
www.rakuten.ne.jp
There are numerous forwarding services that give you a Japanese address that you'd have your tools shipped tool and then forwarded to the US. I like
Blackship - reasonable rates and allows your to consolidate packages into one.