Buy a city guide and map for Tokyo. For your purposes, the one that concentrates on restaurants and entertainment with a few hotel listings (Time Out Tokyo?) is probably best.

If the subway system intimidates you (it's safe and well-marked in English), stick to the Yamanote (loop) Line, which will take you to Ueno for the National Museum (if that's your thing) or to Shibuya (to see all the trendy young people). If you're willing to try to Oedo Subway Line, take it to Tochomae and view the city from the 45th floor of the Metropolitan Government Building.

But really, it's up to you. Get that guidebook and a map, and see what appeals to you.