The area right around comiket Odaiba/Ariake is a bit pricy I think. But, the event is pretty easy to access if you are staying anywhere along Yamanote line (JR loop line) or the Saikyo/Rinkai line (which shares several stations with the Yamanote).
Some areas worth checking are Osaki, Ebisu, Shinjuku, Ikebukuro, Meguro, Shinagawa, and Omori. I've stayed in Ikebukuro for around Y4,000 a night a few years back and Ikebukuro is a straight shot on the Saikyo/Rinkai line to Comiket.
Summer Comiket 90: Tokyo, Japan
Military Odyssey: Detling, England