There are many ways to do this but this is what’s working for me at hackLAB.hk.

  1. 1st we add the Custom Login by Author: Austin Passy
    1. Go to your plugins and select Add New
    2. Search for Custom Login
    3. Add, Activate, then Choose Settings (Does not have Side Menu Option)
    4. You can add your Logo, Etc. and Save
  2. Add Code to Function.php located at Appearance > Editor then change as specified in comments to customize for you!
  3. Test, Test, Test!

Enjoy!

//Customize this code for your Settings then put at end of functions.php in child wordpress theme, then test with a new email registration.
//

//Custom Email Registration

//Here is the filter for the from name:

add_filter('wp_mail_from', 'new_mail_from');

//Here is the filter for the sender name:

add_filter('wp_mail_from_name', 'new_mail_from_name');

//Here is where the new from email goes:

function new_mail_from($old) {
return 'youremail@gmail.com';
}

//Here is where the new sender name goes:

function new_mail_from_name($old) {
return 'hackLAB | Maker Group';
}

//Next we'll hook into the subject and setup a function to change it:

add_filter( 'wpmu_signup_user_notification_subject', 'my_activation_subject', 10, 4 );

function my_activation_subject( $text ) {

//Input the new subject for the activation email:

return 'Customize me: Your account needs activation.';
}
// Customize email itself and run a function to modify the message.

add_filter('wpmu_signup_user_notification_email', 'my_custom_email_message', 10, 4);

function my_custom_email_message($message, $user, $user_email, $key) {

//Here is the new message:

$message = sprintf(__(( "To activate your new account, please click the following link:nn%snn After you activate you will be able to log in.nn" ),
$user, $user_email, $key, $meta),site_url( "?page=gf_activation&key=$key" ));

return sprintf($message);

}