Depends on your standards. You could get a cheap hotel in Tokyo from $30 a night to up to the stratosphere if you like.
Look at:
http://www.toyoko-inn.com/eng/
http://www.superhoteljapan.com/en/
http://www.kid97.co.jp/~jeh-group/jeh-group.html
http://www.wix.com/astroflight/accommodations
And if you have never stayed in one before, I recommend you spend at least a night in a Japanese Inn or ryokan. There are some inexpensive ones in Tokyo, like the Kimi, the Tama, the Taito and the Tokyo Ryokan. See:
www2.dango.ne.jp/kimi/ryokan.html
www.tamaryokan.com
www.libertyhouse.gr.jp
www.tokyoryokan.com
Transport - depends on where you go. You can get a subway day pass and go all over for 1000 yen or about $10. Or get a day pass for the Yamanote line for about 3/4 of that and take the Yamanote Loop - it goes to many popular places.
Food can run you about $25-30 a day to eat decently. Bars and taxis can kill you if you let them though. Souvenirs? A few bucks each to infinity - up to you.
It'd be sad if you stayed only in Tokyo. At least go see Kamamura, NIkko, Hakone, and the Fuji 5 Lakes nearby. Look for some useful rail passes on:
http://www.jreast.co.jp/e/pass/index.html