There's a BIC Camera and Yodobashi store in Shinjuku. Apparently there's also a smaller e-earphone store there, but I haven't visited that. I might be wrong, though.
I usually go to Akihabara, mainly for the huge Yodobashi there and e-earphone.
There are some smaller audio shops in Akihabara hiding among all the computer related shops or tourist traps.
The Akihabara e-earphone store:
http://www.e-earphone.jp/shop-akb
I also like to find Book-off stores. They mostly sell used books, but you might also find used electronic devices. Last time in Japan I bought a Kenwood MediaKeg MP3 player at a Book-off. There are also stores called Hard-off which are specialized at household items and consumer electronics (but those are more rare). Most Book-off have some electronics stuff and you might be able to find something audio related.
Here's a list of stores in the Tokyo area (scroll down):
https://www.bookoff.co.jp/inbound/index.html#shopList
Yuin PK2 is a good advice. However, sub bass isn't very extended and it usually costs around $50.
There's also NiceHCK DIY PK2 which uses the same housing as Yuin uses.
NiceHCK DIY Graphene old version has got good sub bass extension and a slight tendency to be bright (but I'm sensitive) but is also an upgrade from Monk+.
Finally Moondrop Nameless. It is quite neutral with pretty good extension at both ends for the price.
All three can be bought from Ali Express for around $25. Also all are slightly smaller than Monk+...