I'm fortunate to have visited Japan five times. I love Japan, the people, the architecture, the gardens, Japanese artwork, the food, and drink, especially Sushi. I love Sushi. I live for Sushi. I am sure that in a past life I was either a whale or a Sushi Chef.
Tokyo, as I am sure you know, is a very expensive place for visitors. However, once you venture off of the tourist path you will find some inexpensive eateries and interesting sights. But most importantly, you will find warm and friendly people, although your conversations will be somewhat truncated because English is not very common. (Trust me on this one. Take directions written in Japanese and hand it to your taxi driver. Say nothing as you hand it to him, and do not ask any questions about anything especially as you head off to your destination, least he thinks you want to go down that quaint looking street instead of following the directions you just handed him.) Also, do not point at anything under the glass case at a Sushi bar unless you are prepared to eat it, (again, trust me on this one).
Tower (great view of the city)
Ginza Strip (wonderful place to people watch, too expensive to shop)
Takanawa Prince Hotel (inexpensive, friendly, and comfortable)
Sushi Bar in the Basement of the Takanawa Wing Shopping Center (friendly chefs)
Food Court in the belly of the Tokyo Terminal (amazing amounts and types of food)