You're going to be in freakin' Japan! Don't waste your time at knife shops, see an awesome temple or something. Seriously. It used to be different, when you could only find the most special and elusive stuff in Japan. But the internet has changed all that. Now you can find the exact same junk online for probably a better price than in a Japanese retail store. If you can navigate Japanese websites and get stuff shipped to you, that's another story... but then you probably wouldn't be asking here.
That said, if you're in Osaka, stop by the Ichimonji store. Their display is awesome, they're friendly to non-Japanese speaking tourists, and you can handle any knife you want. It's very close to the Namba train station, so you'll likely be passing through anyways.
Sorry to JCHine, but don't go to that place in Kyoto, unless you're a single bevel hipster who needs a brand no one has ever heard of before. Aritsugu is overpriced but the Nishiki market makes it an overall awesome experience. The knife museum in Osaka is cool if you're reeaaaaalllly into knives, but not worth the trip to Sakai (for a US analogy, NYC : Newark :: Osaka : Sakai)
No idea about the Tokyo stores... Where are you going to be in Japan exactly?