I couldn't find the preferences menu for Nautilus file manager in Gnome 3. But the gsettings command works :-)

To set the default sort order to the file name:

gsettings set org.gnome.nautilus.preferences default-sort-order name

To show directories first:

gsettings set org.gnome.nautilus.preferences sort-directories-first true

Hint: In Gnome Shell, application menus are in the system menu, at the upper left of the main display.