I uninstalled Geary but for some reason it still shows in the Messaging Menu with a "No" symbol as an icon. I tried restarting.
Under /usr/share/indicators/messages/applications there are only Pidgin and Thunderbird.
I don't understand why or how Geary is still showing in the menu. I've attached a pic of the menu with the applications folder open as well.
I figured it out myself. I installed dconf-editor
sudo apt-get install dconf-editor
And navigated to com > canonical > indicator > messages
There, you'll find a value called "applications". Within this value are applications between the [ ] brackets separated by commas. geary.desktop was here along with thunderbird.desktop.
So I changed
[thunderbird.desktop,geary.desktop]
to
[thunderbird.desktop]
And now the Geary menu item is gone.