Where to buy a Nintendo Switch?

You should go to a big electronics store, like Yodobashi Camera for example. They have a lot of branches all over the city. Hope you're able to buy one.

http://www.yodobashi.com/ec/unite/globaltop.html

Take a look in bic camera as well: http://www.biccamera.com/bc/main/

I believe in smaller areas, smaller shops or smaller cities it could be easier to find as  these big stores are usually very crowded and the systems go fast!

Try searching for areas around tokyo and go to shops near their main stations there. for example if you go to Kashiwa, you may be able to walk around the are a of " Kashiwa station" and find many electronic shops or game shops, even a bic camera. You might get lucky there.