This is the expected behavior under modern versions of Ubuntu.
According to the online documentation the little 'gear' icon will not be found in the expected place at the right of the toolbar with current Ubuntu, using either GNOME shell or Unity:
The Preferences option is available in either Geary's application menu
or the gear menu in the upper-right of the toolbar. (The location
depends on the install desktop shell. For GNOME Shell and Unity, the
application menu is available near the top-left corner of the screen.)
So under Unity or GNOME the 'Preferences' menu for Geary can be accessed with the keys Ctrl+E while the 'Accounts' menu can be accessed with Ctrl+M. Both menus are accessible by mouse from the top left corner of the screen. But no 'gear' icon...
The screenshot below illustrates the available access: