I voted for Ueno because i like the Area. I than saw that you put kichijoji up on your list and that would definetly be my top spot for living in Tokyo. I have lived close to kichijoji (Inokashirakoen) for 2 month and it is a really nice area. It is quiet, very safe, not to many tourists (at least foreigners), has any shop you need and the Inokashirapark is very nice.
The Park has a small lake, is nice for running in the evening and has a craft market every weekend.
And if you live just a little bit away from the main station the prices drop. I stayed at Oak-house (Guesthouse style) wich was quite nice but id recommend a appartment if you are staying longterm (lets say more than 3 month).
I found this site along my searches
Tokyo Apartments -Reasonable Apartment Accommodation Guesthouse however dont have any experience with it!