Handly AppleScripts to manage OS X notifications. (Use in Automator, bind to keyboard shortcuts via BetterTouchTool, etc.) Inspired by http://apple.stackexchange.com/a/155736

notification-actions.applescript

# Close all notifications

my closeNotifications()
on closeNotifications()
	tell application "System Events" to tell process "Notification Center"
			set theWindows to every window
			repeat with i from 1 to number of items in theWindows
				set this_item to item i of theWindows
				try
					click button 1 of this_item
				on error
					my closeNotifications()
				end try
			end repeat
	end tell
end closeNotifications

# Dismiss only the top-most notification

my closeNotification()
on closeNotification()
	
	tell application "System Events" to tell process "Notification Center"
			click button 1 of last item of windows
	end tell
end closeNotification

# Click top-most notification

my clickNotification()
on clickNotification()
	tell application "System Events" to tell process "Notification Center"
			click last item of windows
	end tell
end clickNotification

I believe this solves the looping issue:

tell application "System Events" to tell process "NotificationCenter"
	set numwins to (count windows)
	repeat with i from 1 to count of windows
		set number_of_notifications to count of groups of UI element 1 of scroll area 1 of window i
		repeat number_of_notifications times
			perform (first action of group j of UI element 1 of scroll area 1 of window i where description is "Close")
			delay 0.5
		end repeat
	end repeat
end tell

Without the delay there seems to be a race condition between the last close completing and the next close being triggered, which halts operation. Other related code I've found online use delay as well (1, 2). Though 0.5 is pretty conservative; you could probably get away with 0.2 on a new or fast machine.

cc @majorgear