Sorry, I only found a Pole Position II, and no topper. The arcades I have gone to are actually not entirely as I hoped. Not a big selection of neither classics nor very new games, but a lot of candy and generic cabs. And most of all crane games.
The best place for classic games was a little arcade in the same mall as Joypolis, and one Sega place in Akihabara. But most places there are most of the same, over and over again.
What surprised me the most was actually the price. 100 yen for one credit, which is a little less than 1 euro. I came from Hong Kong to Tokyo, and in HK the price is 1 HKD per credit. That means it's almost exactly 10 times more expensive in Tokyo than Hong Kong (which on the other hand is extremely cheap), and they mostly have the same games.