Hi,
As far as I know, there aren't any NSX specific shops/dealers that are easily accessible by public transit.
However, here are my suggestions for "must-sees" for the NSX enthusiast in Tokyo.
Disclaimer: Directions are to the best that I can remember, but I am not responsible if you get lost.
It's hard to put the directions into words, but if you have a train/subway map, then it's easier to see. Keep in mind that you need a complete map, or you need to "build" a complete map using several. This is because the public transit system is a hodgepodge of private and state run systems, so it's hard to find them all on a single map.
1. Honda Welcome Plaza
This is Honda's headquarters, and has a small car and motorcycle showroom and gift shop. Sometimes there are special shows and events going on. Take the subway to the Aoyama stop, and they are right next to the subway exit.
Map
2. Mr. Craft
This is the mother of all model/diecast shops. It's 4 floors, and the top floor is a consignment showroom with many out of production or rare items. Take the Yamanote Line to the Ebisu station. I can't remember which exit you need to come out of, but there is a J-phone store across the street from the exit. If you don't see a J-phone store, then it's probably the other exit. Mr. Craft is diagnally across the other street (it's an intersection) from the J-phone store.
Map
3. Super Autobacs
This is a Japanese auto parts and accessories superstore. The highlight of this (in addition to the plethora of accessories) is the 2nd floor bookstore and model/diecast shop. The book store has a wall of drawers full of catalogs/brochures for just about every Japanese car ever made. They have stuff for JDM, European, and US markets, some dating back to the '70s, although the US and European stuff, as well as the older stuff tends to be expensive. You can find lots of memoribilia here. Take the Rinkai line to Shinonome, and you can see it when you come out of the station.
Map
4. Toyota Mega Web
I know, it's Toyota, but it's a really cool showroom with pseudo-test drives, an attached shopping mall and amusement park (for the family, while you are looking at car stuff), and there's an automotive history hall/museum (for all cars, not just Toyota), and a pretty large model/diecast shop. If you are going to Super Autobacs, it's accessible from the Rinkai line, although I can't remember the name of the stop right now. You can't miss it though, because there is a huge ferris wheel. It's also accessible from the "Yurikamome" line. It's the stop right before or after Odaiba, but I can't remember which now. Again, you can't miss the ferris wheel. To get to the Yurikamome line, you can take the Yamanote line to Shimbashi.
Map
5. Kinokuniya Bookstore
This is a large Japanese bookstore. They have lots of magazines and books about many cars, including the NSX. I've been to both Shinjuku locations, and their selection in the automotive section is pretty extensive. Lots of interesting magazines that you've never heard of. They also stock many back issues of the Hyper-Rev series of magazines. I've picked up a lot of NSX related material here. There are two stores in the Shinjuku area. The Main store tends to have more stuff, but the South store is easier to find. Take the Yamanote line to Shinjuku Station. Shinjuku Station is a labyrinth, so make sure you come out the right exit. For the South store, it's in the Takashimaya Times Square complex, on the far side. From Shinjuku Station, exit from the "New South Exit", and it should be easy to find.
South Store Map
For the Main store, you can look at the map and decide if you want to try to find it or not. It's not difficult to find, if you know the general direction, but it's hard to describe in words how to get there.
Main Store Map
6. Macs
This is an NSX exclusive dealer, but I don't think it's easily accessible by public transit. You can see their website, which has a map, and decide if it's feasible to visit:
Macs Website
