Where to stay in Tokyo?

There's so many things to see in Tokyo and not sure the best area to stay there for 2-3 days. Interested in Ryokan, at least for one night. Any suggestions? It's for my husband and I. We are not interested in the shopping area more the historical sites. Thanks!

It depends on your budget more than anything else as most sights in Tokyo are easy to get to from any station on the JR Yamanote line (less confusing as subway as you can see where you are)or a combination loop line plus a short subway trip. Ryokans, especially not too expensive ones, aren't as easy to find in Tokyo as in Kyoto. check www.japanhotel.net for business hotels and a few ryokans to give you some idea of prices, how rooms look like,etc
you need to know too that Tokyo doesn't have as many temples and shrines as smaller towns like Kyoto, Kamakura etc. if you are interested mainly in traditional Japan plus a glimpse of modern Japan the Kansai region is a better bet than Tokyo. Kyoto and Nara are old capitals, Osaka is a very modern metropolis with great shopping and eating choices(I NEVER buy much but you got to check Japanese department stores. their food floor and the floor with formal kimonos, traditional furniture etc. are must see). The Kansai is also Himeji castle, the town of Kobe etc.

follow up:
for cheap to moderately priced hotels and a peek at the life of the average person in Tokyo, especially in the back streets: the districts of Ueno and Asakusa.
for big crowds, big stores: Shinjuku ans Shibuya with hotels that are more expensive than the 2 areas above; cheapest ones are booked months in advance.
not to be missed: Harajuku JR station area: a big park and the great Meiji shrine on one side, on the other Takeshita dori with hordes of young people and often wild clothes then Omotesando avenue with amazing stores (both architecture and goods) the farthest you walk from Harajuku station towards Aoyama.
Ginza avenue, especially in the mid-afternoon, for more great stores, huge lights, the Kabuki theatre etc.
Shinagawa for the remains of the old Tokaido road and the temple made famous by the 47 Ronins but also the new modern Shinagawa with hotels in various price ranges.Odaiba, an artificial island with very interesting sights. There are also other areas where the old Tokyo can still be seen..

Try these two sites:

www.tctv.ne.jp/sawanoya - a traditional ryokan near Ueno

www.jpinn.com - look for ryokan in neighborhoods mentioned above by redfrog

Another two Ryokan in the Ueno area:

http://www.katsutaro.com/ryokan_index.html