The question to ask is: what prevents you from paying for one zone and then traveling in all three? The answer is, basically nothing.
It's good to hear that buses in NYC now accept MetroCard. I gave up on buses there when you had to have coins or tokens - which, as a visitor, I never had. (Not that I much felt the need to use the bus there, as I stayed almost exclusively in Manhattan, and the subway served me nicely.)