TamaDepa in Tokyo is near Harajuku station. Harajuku station is on the Yamanote line, a couple of stops counter-clockwise from Shinjuku. There's a map of how to get from the station to TamaDepa here: http://tamagotch.channel.or.jp/tamadepa/
It'll be a small, cramped shop, full of little kids and their distressed parents. The music will quickly become annoying, and you'll still hear it in your mind for much longer than you thought possible. I highly recommend you go there on the first day you arrive... because within a few days you'll want to go there again.
Tamagotchi toys and merchandise should also be easy to find in major department stores such as Ito Yokado, Aeon, and toy stores such as Toys-R-Us. The larger of the Bic Camera shops also have a toy section where you should be able to find Tamagotchi toys etc.
You might be able to find older Tamagotchi toys and goods in Hobby Off. Hobby Off sells used toys & character goods, but they're usually not located close to subway / train stations.
If you're going to be in Japan (at the same address) for two weeks or more, and you have a Japanese friend who can help you, you may be able to find some good deals on auctions.yahoo.co.jp (Japanese equivalent to ebay.) Look for auctions ending with enough time afterwards that the item can be shipped to your hotel. You'll most likely need a local Japanese helper to assist you with making the payment. The most common forms of payment are cash transfer through a postal account, and cash transfer through a bank account.