As Charles suggested, you should be able to find Nikon Goods at these three mejor retailors. In and area called "Shinjuku", you can find all these shops plus the Nikon Plaza (service center).
If you would like to try some smaller individual shops that deal with second hand stuff, this would be of some help:
If you plan on buying "duty free" you will need your passport and (maybe) the out-bound airplane ticket. Anything "hot" [like a Nikon D2X body] will not be discounted, the photo store managers have Internet knowledge and know the prices elsewhere in the world. Some 'stuff' may be less costly in New York City....
Along with the Shinjuku district, a few camera shops may be found in the Ginza area of Tokyo.
If you want to pay lower than the price tag, bring cash. Cash is still a very common currency in Japan and they will often offer a lower cash price. The dollar is falling against all major currencies right now, last I checked you're only getting about Y113 per dollar so don't expect much of a discount. When I bought my new SB-28 in the DenDen Town district of Osaka (their electronics shopping district) I think I saved about $50 or so over buying it in the states. And they will give you an international warranty card as well as the manual in English.
I didn't declare the flash on my customs statement on the way home on the plane, but I think if you purchase more than $600 or so you should bring the receipt and prepare to declare it. You may have to pay a duty tax, I'm not sure.
I would hold off on all major purchases of new equipment in Japan as I think it will always be available cheaper in the States at current exchange rates.
you will not get a better deal on new equipment in Tokyo but the prices are better for accessories and for used equipment. I got some Nikon L37C filters for 1/4 of the price here in Canada and Nikon circular polarizing filters for just under 1/2 the price. I was surprised to see that the prices for compact flash cards were the same or higher than here. cb