Disabling the module providing the content type should be the first step. If the content type was provided by a feature, you'll still need to delete the content type.
For a well-made Feature, the ability to delete a content type will come after the Feature providing it is disabled. This is preferred over deleting a content type out from under a feature, as current functionality or future updates to that feature may require the content type.
Note that you can disable feature modules (admin/modules) even when the the Features interface is (rather foolishly) claiming it cannot disable a module because of conflicts.
And if you don't want to do anything through the interface, and just want to do code, here's an example of an update hook that will disable the Commons Wiki and Posts Features and then delete the content types they provide.
<?php
/**
* Remove unused features and content types.
*/
function example_update_7001() {
// Delete one (spam) piece of wiki content.
node_delete(2731);
// Disable Feature modules.
module_disable(array('commons_wikis_pages', 'commons_wikis', 'commons_posts'));
// Delete content types.
node_type_delete('wiki');
node_type_delete('post');
}
?>