Takarajima 24 Ueno Main Branch

Cheapo Article: Takarajima 24 - The Internet Cafe that REALLY isn't
Area: Ueno
Access: 125 m from Okachimachi Station Yamanote Line (JY4)Keihin-Tōhoku Line (JK19)
219 m from Ueno-okachimachi Station Oedo Line (E9)
245 m from Ueno-hirokoji Station Ginza Line (G15)
Address: 1F - 5F Kaneko Bldg., 6-9-24 Ueno, Taito-ku, Tokyo [map]
Phone: 03-5812-3252 03-5812-3252

Takarajima 24 is a chain of internet/manga cafes with private rooms.  You can put your stuff there, lock the door and then go out for the evening.