You have to know where to shop, but in general lens prices are higher in Japan than in the U.S.
Map Camera as described above is great not only for used equipment, but it has some of the best prices for new equipment among "real" camera shops.
However, if you really want to find a good deal, you have to do a little searching.
http://kakaku.com is similar to pricegrabber.com or shopping.com and the best price for a D3x there is currently about 670,000 yen. This is over 100,000 cheaper than the current price at Map Camera.
The problem with the 200-400 and other exotics is that they are often out of stock, so they aren't listed at kakaku.com. In fact, it is hard enough to find them at Map Camera, Yodobashi Camera or any of the other big camera stores, so you can't expect to find them for a bargain.