I used to harvest cocoa beans with a simple pulse of water that would travel down the trees and carry all the beans down into hoppers. However, I built the old harvester on a SMP server I play on (play.ozonecraft.com, part of the OzoneCraft Network) and one of the mods wanted to see it in action. Needless to say, he wasn't impressed. He thought the trees would move.

So, after hearing him say that, I set out to build a harvester that moved the trees instead of the beans and this is the result. You press the button and the trees get pushed upward and then back down, effectively shaking all the cocoa beans off where they are collected by the hoppers.

Here's how it works: when you press the button, a 1 wide monostable circuit sends a quick pulse to a sticky piston holding a redstone block. This quickly pushes the redstone block over to a dust and then pulls it back again effectively sending a quick pulse into the dust witch travels into the bottom pistons, raising them up. Then the signal travels up the torch ladder and is delayed a tick before reaching the top pistons, giving the bottoms pistons time to retract, then sending the trees back down ready to be replanted on.

Additional Notes

In my SP test world, the glass in the front was needed to prevent the cocoa beans from flying out all over however, in the SMP server I play on, the glass isn't needed at all. So you may or may not needed the glass wall if you build it.