It is hard to say because there are so many kinds of ramen, preferences be totally different depending on the person!
I see lots of tourist lining up for Ichiran, Ippudo, Komen, and AFURI. Of these four, AFURI is my favorite.
I like lighter ramen rather than thick, heavy, oily ones.
AFURI is considered to be a rather "healthy" type of ramen, since it is non-oily and also has a vegan ramen. YUZU-SHIO ramen is good, but also tsukemen, the dipping type of noodle, was great. AFURI has multiple branches within Tokyo, such as Ebisu, Harajuku and Shibuya.
Another one I like is Kaijin in Shinjuku. Kaijin means "god of sea" and as the name indicates, the place is specialized in fish soup ramen. What is notable at this place is they use different fish each day to make the soup, depending on which one is the fresh kind at the season. So you will be able to have different tastes each time. If you come here, order an onigiri (rice ball) and put that into the soup after you finish the noodles! You can enjoy a delicious risotto with seafood soup :)
The soy sauce ramen we ate the other day was delicious.
It is located in Yushima near Asakusa and Ueno. It is a shop named Daiki.
I also like ramen shop selling unusual soup with sake liquor called Kazami in Ginza.
Others are gathered here.