You could also try a capsule hotel if you're able to sleep through some noise.

There's a "cabin" hotel in Tsukiji which seems popular for those trying to catch the tuna action without an early morning taxi ride.
https://www.tripadvisor.com/Hotel_Re...ure_Kanto.html

Several new hipster/themed hostels have opened up in Tokyo, too. Some are attached to bars, yakitori, bookstores.
http://www.japantimes.co.jp/life/201...ling-not-know/
Most use a capsule/pod configuration.