If you have a friend on a US Military base, they can buy one at the PX for you. Otherwise, there are a few shops in Akihabara, Tokyo near the station that sell "import" (as in re-imported to Japan) systems and games. I haven't checked lately though, so they may not have any next-gen systems in. If you do it the domestic way though, it's going to be at least 25 to 50% more expensive.
You'll probably not have an easy time finding one...there are not at all easy to find in the US...I've yet to see one in the 'wild' as of yet (ie, one on the shelf available for purchase) here in the US. Ebay may be an option, although I would suspect not that many buyers will be willing to ship to Japan.
If you are in or near Tokyo, you might want to check the import stores...There's two I know about in Akihabara...one is on the four or fifth floor in a building on the street just north of the sobu line embankment...I think its called game hollywood or something like that....there is another one north up on Chuo Dori on the left hand side...I think it is just a little past Sofmap zero...its up on a second story but the stairs are visible from the street...on the stairs are written various game system names in English and they typically had a sidewalk sign that says something like import games this way up with I think had a picture of a US football video game like NFL 2K for the dreamcast....it is just south of the Messe Sanho main store if I remember correctly
Well, of course, now that I've written this I bothered to google 'game hollywood'+akihabara and I found this link covers everything I've already said and more like weblinks, so you could probably call and ask if they have one.