Change new user notification e-mail body.

functions.php

<?php

add_filter( 'wp_new_user_notification_email', 'gist_change_new_user_message', 10, 3 );

function gist_change_new_user_message( $wp_new_user_notification_email, $user, $blogname ){

	$wp_new_user_notification_email['message'] = "This is the new mail body.\r\n\r\n"";

	return $wp_new_user_notification_email;

}