This small museum, designed mostly for kids (and rather dry considering its subject), covers the history of animation in Japan and its digital future. Temporary exhibits sometimes show cel art from major animators; there are also light tables (where you can practise drawing) and a manga and anime library. It's sometimes closed in between exhibitions; check the website before heading out.
Take any bus from stand 0 or 1 outside the north exit of Ogikubo Station to Ogikubo Keisastsusho-mae (five minutes, ¥210). Double back to the traffic light and turn right. Otherwise, it's a 20-minute walk from the train station.