EDIT: I've got a friend going to Japan this weekend and wants to eat this so I'm making this guide a lot more detailed. More detailed instructions are at the bottom.
To me, Fuunji in Shinjuku was like the top of the tsukemen food chain. I could not imagine a better tasting tsukemen, until I went to the new Ittou branch in Shin Koiwa.
Ittou is famous for its fish based tsukemen which is good but not worth the one hour wait. With the new shop, I haven't really encountered any queues the 4 times I went there during this trip.
I noticed something different in the menu. チャッシュ極濃厚煮干しつけ麺。The name translates to charsiu extreme thick, dried sardine tsukemen.
And it tastes as good as it looks. Super creamy soup and three layer pork that is do die for.
The standard protion is a bit too little but the larger portion chuu 中 is a just right. You need to get an extra ticket to upsize. I do not recommend the largest portion 大盛り unless you want to feel super bloated. I recommend getting the normal portion with karaage or gyoza as a side dish the soup got cold towards the end of eating the middle portion.
You can find the map here. There are two Ittous in Shin Koiwa so you want to go to the one south of the station. Its only a few minutes walk and my favourite drinking estalishment Hotaru is nearby.
This is the map from the South exit of Shin Koiwa station. Its very easy to follow.
Give your tickets to the staff member on your left. He will say because it will take some time so just nod your head and have a seat and wait patiently for your tsukemen. There will be cups on the counters and tables for you to pour water for yourself.