[UPDATE]: Yosemite support has been added.

I can’t guarantee results, but this has seemed to work for me.  The following commands disable the Apple App Store notifications that appear in OS X:

NCutil.py --remove com.apple.maspushagent NCutil.py --remove _SYSTEM_CENTER_:com.apple.storeagent

I believe removing the noticeboard and app store will also suppress notifications.

NCutil.py --remove _SYSTEM_CENTER_:com.apple.noticeboard NCutil.py --remove com.apple.appstore

Disable These Annoying Notifications With NCutil.py

Normally, you cannot disable these because they do not show up in the Notifications pane of System Preferences, so I decided to write a command line utility that would allow you to do this called NCutil.py.