Priceline can usually be played to get you into the Crowne Plaza in Ikebukuro for under $120/night. Small room but decently located to get to and from Narita -- I'd recommend taking the Keisei line from Narita airport to Nishi Nippori and switching to the Yamanote line to Ikebukuro. The hotel is right next to the station on the southwest side.

The only other international hotel chain that Priceline seems to regularly get is the IC Tokyo Bay, which is not very conveniently located for a short MR.

There is also a Hilton near Shinjuku but it will be considerably more expensive.