Hi Catlyn!
Are you looking to buy them new or used? I recommend getting a used one because they are usually in very good shape and you pay less.
If you want to buy a new one, you could go to either the Apple Store in Omotesando, Yodobashi Camera (everywhere, you can find in Akihabara, Shinjuku, Ueno.. in many places) or Bic Camera (you can find in Shinjuku and Akihabara,
All of them should have the same price.
If you want to buy a used one, look no further than Akihabara! You can take a look at any of these shops: https://www.google.co.jp/search?q=akihabara%20shop%20for%20used%20phones&rlz=1C5CHFA_enJP775JP775&oq=akihabara+shop+for+used+phones&aqs=chrome..69i57.4554j0j7&sourceid=chrome&ie=UTF-8&npsic=0&rflfq=1&rlha=0&rllag=35700166,139771594,202&tbm=lcl&rldimm=16194934466594747690&ved=0ahUKEwiL8tW1srTZAhWEvLwKHY9WAJUQvS4ISDAA&rldoc=1&tbs=lrf:!2m1!1e2!2m1!1e3!3sIAE,lf:1,lf_ui:10#rlfi=hd:;si:16194934466594747690;mv:!1m3!1d2666.312361094521!2d139.77250655!3d35.6997504!2m3!1f0!2f0!3f0!3m2!1i86!2i158!4f13.1
I hope it was helpful!