Another option, which uses Keyboard Maestro to run an Applescript is detailed here: http://genuinecuriosity.com/unnotify
I have it mapped so that I hit Command Option 0 to clear all open alert dialogs.
Basically, I have created an Applescript to click the first button on all open alerts (typically Close), and does that until all alerts are cleared. You can use the Applescript directly through Keyboard Maestro (as described in my article), or you can create a Service with Automator (this is a little more finicky due to Accessibility permissions requirements).
The full Applescript is included in the article, along with a screen grab showing the setup in Keyboard Maestro.