Did you mean dinner? I would get on booking Takazawa right now as they've become so popular (and a bit stuck up) when it comes to reservations. Better to do it as early as you can. Those last two places will definitely show your son some exotic, different ways to eat food. He's in for a treat...

Tokyo hotel:
Andaz Tokyo would be my choice. HR Tokyo is great value but Andaz is just something else. You must try their nutella brioche French toast. It's to die for!

Kyoto hotel:
You need to go out the west exit and find the MK taxi stand across the street. You tell them your name and they will take you to the hotel. The hotel reimburses the taxi company. You needn't worry about it.