WP_Query_Multisite is a subclass of WP_Query, WordPress' post querying class. The class does everything behind the scenes, so the only change you make to query multisite is the in the class declaration expression.

Example usage:

$query = new WP_Query_Multisite( array( 'post_type' => 'post' ) );

while( $query->have_posts() ) : $query->the_post();
    echo $blog_id . get_the_title() . "<br>";
endwhile;

wp_reset_postdata();

To modify what sites are queried, create a sites key in the $args in the constructor parameter, with a sub-element of either sites__in or sites__not_in, which will be an array similar to posts__in in the WP_Query object.

Example usage:

$args = array(
	'post_type' => 'post',
	'sites' => array(
		'sites__in' => array( 1, 2, 3, 5 )
	)
);

$query = new WP_Query_Multisite( $args );

while( $query->have_posts() ) : $query->the_post();
    echo $blog_id . get_the_title() . "<br>";
endwhile; 

wp_reset_postdata();

Alternative

We do want to suggest that this version / fork uses pre_get_post and may be a better solution for you. This way you can keep using the good 'ol WP_Query without editing any theme files.
https://github.com/miguelpeixe/WP_Query_Multisite