I reckon that individual restaurant recommendations are not the best way to go in most cases, but telling you to have ramen in Tokyo without pointing you to the right places is like telling you to have texmex in the Bay Area without telling where to go: you may end up eating at Taco Bell and having a bad experience.
The thing about ramen is that, besides it having many different traditions (i.e. Hakata style, Yokohama house style), every restaurant strives to develop its own personality. In that sense, no ramen bowl is cooked the same, and where you eat it can matter significantly.
Here are some recommendations of where to have some good ramen in Tokyo (from a ramen foodie who lived there for 5 years):
Jangara Ramen in Harajuku has a great pork based soup.
Botan in Ōtsuka has one of the best Kyūshū style pork based soups in the capital.
Ore no Sora, with stores in Takadanobaba and Ikebukuro has a blend of fish stock and pork soup that tastes like heaven, if you can tolerate the hidden notes of bonito flakes on their broth.
Ivan Ramen, by the karate kid of ramen Ivan Orkin, is the best non-Japanese ramen chef in the world.
Nakamuraya in Ebina (outside of Tokyo but totally worth the trip) is the legendary ramen restaurant in Japan.
Other than that, Ippūdō is a chain that makes decent ramen if you are not too picky, and they have stores all over Tokyo.
I don't have time to translate the Japanese links, but believe me, they are worth the time using google translate or asking a Japanese acquaintance. These are not just my personal favourites, but they are also restaurants that consistently rank among the best in Japanese food magazines and TV programs. That is how I came to know most of them.