Take a look at Administration Menus. You will be removing the current menu page and adding it as a submenu page. Your callback to ‘admin_menu’ action must have a larger priority number than that used by the plugin otherwise there will not yet be a menu to remove.
You’ll need to examine the plugin add_menu_page() code to know how to add it as a submenu. A rather hacky alternative exists. Examine the structure of the global $menu using var_dump() or print_r(). It may be possible to assign the plugin’s menu item in the array directly to the Settings menu item. Once assigned, unset the original item.