[Update, Jan 14 2020] The venue is under rennovation until further notice
A bookstore has never been as one-stop as this: Tsutaya Book Apartment & Book Lounge has got to be one of the most unique places to stay (and do some reading) in Tokyo. Occupying three floors in the Shinjuku Minim building, it houses a sake bar in the basement, a co-working space on the fourth floor, and private sleeping booths complete with shower facilities on the fifth and sixth (for women only) floor.
This being in Shinjuku, it's also perfect as a crash pad for folks who have missed their last train home after a night of bar-hopping. And yes, there's free Wi-Fi for guests.