System Preferences » App Store. (It is there in Mavericks – look for the blue circle with the big, stylized “A” in the second row from the bottom.
This reportedly works in Mavericks. Dunno if it works in Yosemite.
sudo defaults write /System/Library/LaunchAgents/com.apple.notificationcenterui KeepAlive -bool False
You might be able to control-click on the Update button for the update in App Store, and select Ignore Update.