I always use the CitiBank ATM as I am a CitiBank customer and it's right on the way to the elevators down to the JR ticket office and the N'Ex train into Tokyo station. There have been a couple of times when there was a line, but it's never been excessive, and I've never seen it down, though I'm sure that it happens.

I don't know if there are any CitiBank ATMs in Tokyo, but I do know of one in downtown Kyoto. Again, very convenient for getting local currency without paying a "service" fee.