The Akibaland tour lead by a female guide in maid cosplay should cover the otaku angle.
http://otakumode.com/sp/visit_japan/akihabara/a017

There's a lot of different genres of manga and anime. Instead you having to figure them out and which stores to visit to satisfy otaku hoarding tendencies, let the otaku specialists do it. Also, it can be pretty expensive/overpriced to get a photograph of/with a cafe maid, so a cosplaying bilingual guide really is the best of all worlds.