I have discovered the Crown Plaza Metropolitan in Ikebukuro. It is right next to the JR Yamanote station and major subway lines, costing only about Y12,000 if you are a member of the (free) Holiday Inn Priority Club. Throw in free high speed internet access (be sure and ask in advance for this, as not all rooms have it) and this one can't be beat.

http://www.sixcontinentshotels.com/h/d/CP/hd/tyomp

(by the way, the Holiday Inn Commercial Center was a dump of a place... it was probably no longer deserving of the name)