これでうまくいくと思います:
$users = DB::table('users')
->select( array('users.*', DB::raw('COUNT(lead_user.user_id) as LeadTotal'), DB::raw('COUNT(user_inventory.user_id) as InventoryTotal') ) )
->leftJoin('lead_user', 'users.id', '=', 'lead_user.user_id')
->leftJoin('user_inventory', 'users.id', '=', 'user_inventory.user_id')
->where('users.is_deleted', '=', 0)
->get();