Accommodation Help for Tokyo/Kyoto

Okay, so this might be a weird question for me to ask, but I have friends coming to visit me in early April and I am looking at meeting them in these two places.

The problem is, I don't have much experience of what areas are decent for hotels. Despite being in Japan for 6 months, I have only been in Tokyo for four days (and accommodation was sorted by my employers) and in Kyoto I stayed at someone's house.

I know quite a few GRcadians have visited Japan or have lived there, so does anyone have any recommendations?