Just in case you want a regular hotel in Tokyo (not business hotels) around $100~$110 range, I often use this Prince hotel in Shinagawa, which is located very conveniently. (unless you must stay in Shinjuku area only.) http://www.princehotelsjapan.com/shinagawaprincehotel/
(and don't have to worry about sneaking in an extra accidental guest or two ) Shinagawa is only a few stations away from Shinjuku by JR Yamanote(Green circle line on map) train, and the hotel is almost right at the station.