As has been said above, things like airfare, flight schedule, hotel availability will decide this for you. Ultimately I don't think it matters a ton as angra says.
But with those things aside, I'd say Kyoto first, Tokyo second.

Tokyo is amazing, but it can probably be daunting and overwhelming to someone who's never been to Jpn. Kyoto's much smaller and more tourist-oriented through and through, and so a better place to get your feet wet in terms of figuring out how things work in Jpn. Once you get a bit acclimitized and more confident, you will likely get more out of your time in Tokyo and realize that Tokyo is 10x more awesome than Kyoto (sorry just had to throw that in there).