06-05-2010, 01:57 PM
Cheapest hotel in Shinjuku would probably be
Shinjuku New City Hotel
4-31-1 Nishishinjuku Shinjuku
Tokyo, 160-0023 JP
Tokyo: Shinjuku
But that will run you $70-$80 a night, might want to look into travelocity.com and see about bundling your flight and hotel and play with some options.
I used them (travelocity) for my trip and everything was perfect.
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