Messages app showing unread number after deleted message. Can remove/reset?
Two options:


Close Messages.app, then in the Terminal killall Dock. This worked for me.
Identify the message that Messages believes is unread (hover over icon in Dock) and delete it on your iDevice(s).


From here: http://forums.macrumors.com/threads/unread-messages-badge-on-mbp-is-stuck.1806575/

Also, this seems to be a duplicate of Why does Messages on OSX always show unread messages?