I have been there twice now, here's the scoop
J&L, back when I visited NYC in 1996, they only had one main store down in the basement mall on Elizabeth St, there were 2 other stores and supposedly, these are owned by the relative of Leslie (boss of J&L). One of the stores in the basement is Penguine Village where I got a brand new copy of Metal Slug X import for $200 (this was back in 1999), I used my credit card to buy the game, and they went to J&L to charge the card.
When I went back again in 2000, J&L opened another store right by the corner of Canal and Elizabeth, the store is much bigger and much more visible from visitors. In late 2000 when I went there, Leslie had over 100 home carts in stock, before you celebrate, look on the price tags first, some games are $500+ range. There's another import game store closer to McDonald, on the 2nd floor of the Chinese shopping mall, I don't think they carry home carts but they do have some NGPC stuff.
Another cool store is Multimedia1, I know the manager, Greg Wilcox, who frequent my TurboGrafx club, he normally works there during the week and is very cool, should talk to him in person. I didn't know Multimedia1 stopped carrying NG home carts, back in late 2000 they still have quite a few in stock, but they have pretty much everything else from Odyssey to current systems.
The other good place I can think of is Game Express on 32nd St (the one right in front of Madison Square Garden), no NG home cart (they used to, got some from there) but good selection of DC games, including rarer domestic DC titles, I believe they still have some NGPC stuff there.
