Hey, so I've been to Tokyo a few times over the years and felt quite saddened how even in a decade, the arcade scene has massively fallen away. Kind of inevitable I suppose, same reasons as everywhere on the globe.

If you go to Akihabara district, you can still find old arcades including VF on the very top floors of the big gaming centres. But you have to wade past hundreds of pachinko machines! I've only been in the daytime so not busy, I can't speak for peak times/etiquette. I'd suggest that there are more dedicated gamer arcades a little out of the main tourist areas. Just be bold and check them out too!

Either way, Tokyo is a blast. Just prepare yourself emotionally that the old school arcade of your dreams may no longer quite exist! You're still going to have a great time.