The lockers that I know about in Kyoto station are on the side that exits to the center of town, but they are down one level (by escalator) from the ground floor. There are two banks of lockers, on either side of the escalator, whichever escalator you take. I've managed to find a suitcase-sized locker the few times I needed one but I have always had to search.

Oh, you went to Tokyo and said you saw all the major sights but skipped Akihabara? Shame on you!