Soba House Hototogisu in Hatagaya is reportedly very good (
Tokyo Time Out).
Yamaguchi near Waseda is also a solid example of shoyu ramen with a chicken-based soup stock.
I also like
niboshi ramen, which uses dried sardines for the soup base.
Nagi in Shinjuku does a good version.
This blog has a good roundup of Tokyo ramen in English.