@Jeffrey’s answer is correct is you are the one registering the post types, simply remove the support argument for comments
.
But if you want to remove it from all custom post types (that may be registered by plugins too) you can do:
$cptslugs = get_post_types( array('public'=>false, '_builtin' => false) , 'names', 'and');
foreach ($cptslugs as $cpt) {
remove_meta_box( 'commentsdiv', $cpt, 'normal' );
}