I would honestly be surprised if there were,
Not just Japan, but anywhere, Stand up is in the language of the locals.
If you want some comedy though,
Here are some good uns you may have missed
I love Hans Teeuwen, he absolutely makes me fall of my chair.... although he can go too far with his jokes.
I actually found this on google: Tokyo Comedy Store and they have shows at the hobgoblin in Shibuya as well. (there are actually some video's on youtube about it as well if you search for "Tokyo Comedy Store"... I just hope it isn't the standard " I am a gaijin and get upset because they keep telling me I can use chopsticks well jokes")
I would think just where there are the largest English speaking populations. Maybe Tokyo
possibly one or two here or there in Osaka. Perhaps you should start writing your own
material