If you have Gnome 3.2, you simply click on your user menu at the top-right and flip the Notifications switch.
On Gnome 3.28.4: At top-right corner of screen: Settings > Notifications > Flip the switch:
From CLI:
gsettings set org.gnome.desktop.notifications show-banners false
I was frustrated about this too.
Install dconf-editor, run it, and go to
org.gnome.empathy.notifications
and disable the first three options (signin, signout, away).
