There are many great ramens in Tokyo. Most famous ones to tourists are Ichiran and Ippudo, I think. I have seen queues of travelers many times.
I like AFURI. AFURI is in Ebisu, Harajuku, etc. Their concept is "healthy" ramen. Very light soup feels great. They also have a began menu, too.
Kazami in Ginza had a very unique ramen. Sake lees! In fact, it was good! Maybe you should try one :)
t's tantan in tokyo station