if u havent checked it out already,
japan guide is a great resource for most things u want to do in japan. the site itself and the forums are good for finding out things to do.
in tokyo, id suggest visiting tsukushima's "monja" street. its a quirky 1/2 lane street with a bunch of different monjayaki restaurants. theres also a small store there selling amazing fresh melon pan.
in shinjuku, id suggest walking through omoide yokocho (memory lane or "piss alley") right beside the main JR station. theres a lot of great izakaya/horumon/yakitori restaurants in a small confined area.
if ur bored in shinjuku at night, id suggest walking through kabukicho to see how the red-light district is there. some great restaurants in the area and just an interesting sight overall. just ignore the black/sri lankan/japanese guys trying to hustle u to go to soaplands/kyabakura (cabaret bars)/strip clubs/bars.
if u have the time, take a daytrip over to yokohama as well.