Please check my "Card Shops in Japan" page before planning a trip to this store to verify that it's still where it was when I visited.
The first card shop I went to on my trip was the Mint Shinjuku store. It's located a few blocks east of Shinjuku Station in on the second floor of the Adhoc building on Yasukuni-dori, the main road through Shinjuku (see the map at the end of this post). There's a big sign for the store on the side of the building - this is apparently Mint's flagship store:
Here's the entrance to the shop inside the building:
A lot of Mint's stores that are located in shopping malls share some common features - limited space and limited inventory. Mint Shinjuku fits that description. What you can expect to find here is the most recent releases - both as unopened packs and boxes and single cards. More expensive cards (autograph, memorabilia, rare parallels, rookie cards) can be found in display cases around the outer walls of the shop. You are unlikely to find any cheap older cards here - although keep an eye out for any odd trays of miscellaneous cards - I don't know if there are any here but I found a couple at other stores that were a lot of fun to go through.
I wasn't expecting a whole lot from this store but Ryan had advised me that I might find good things there. And I did although I don't think I found anything that I wouldn't have found at other Mint stores. I ended up buying a couple of Epoch One cards from last year, a card I was missing from last year's Epoch NPB set and an NPB grab bag.
I paid cash here but I'm pretty confident that they take credit cards (including US based ones). Actually I'm pretty confident all the Mint stores take credit cards.
Here's a couple photos of the interior of the store:
Here's a map of the store's location: