Continuing south from the Science Museum brings you to the National Museum of Modern Art (Kokuritsu Kindai Bijutsukan). The permanent exhibition here features Japanese art from the Meiji period onward, but check the website for special exhibitions.
Hold onto your ticket stub from the National Museum of Modern Art, which gives you free admission to the nearby Crafts Gallery (Bijutsukan Kogeikan), housing a good display of crafts such as ceramics, lacquerware and dolls.
South of the Budokan is the Science Museum (Kagaku Gijutsukan), a decent rainy-day stop for those with children in tow, especially since most exhibits are interactive. An English booklet is provided with entry.
The National Museum of Western Art (Kokuritsu Seiyo Bijutsukan) has a respectable, though rather indifferently displayed, permanent collection. It frequently hosts special exhibits (admission varies) on loan from other museums of international repute.