Last Sunday i went to Edo-Tokyo Museum with my english class' friends, Denny sensei, and Loida sensei. For those Japanese in my class, Edo-Tokyo Museum was boring. But for me, it was interesting. Because i could learn a lot about the history of Tokyo from the explanation of the tour guide. So, the begining of Tokyo was on Edo Era. The leader of Edo had a very strict regulation about the classification of the people who lived in Edo area. In the highest class were the samurai, in the second class were farmers, in the third class were ordinary people (citizens), and the lowest class were merchants.
After the Edo Era, then it changed to the mix era. When the foreigner started
to come to that area. And finally Japanese emperial moved from Kyoto to Tokyo (which means the east side of Kyoto).
And there are still many interesting stories there, so maybe when you're going around Tokyo, you can stop by there.
From Shinjuku Station, take JR Sobu line. Then get off at Ryogoku Station. It's about 3-7 minutes walk from the station to Edo-Tokyo Museum.