For anyone too lazy to go look at the Codex, here it what I used:
// example custom post type is "event"
// example custom taxonomy is "events-category"
function remove_default_event_category_metabox() {
remove_meta_box( 'tagsdiv-events-category', 'event', 'side' );
}
add_action( 'admin_menu' , 'remove_default_event_category_metabox' );