Sadly I've only spent a few days in Shinjuku, and those were the only two ramen joints I hit up. Fūunji is definitely known for their dipping noodles and that broth. If memory serves, Menya Musashi has a rotating menu so that can be fun.

My favorite of that trip was actually the Kio chain in Osaka (cold noodles and beer on a warm summer day were perfect). There are a ton of great resources for sussing out good ramen in Japan, thankfully.

What noticed though was that while all the ramen I tried was better than what I've had stateside, each ramen shop would typically nail one or two things and the rest would be good but not amazing. I never did find an egg as well cooked as I have in the Bay Area.

Also right by Shinjuku, the French bakery was pretty darn good.