Why do I get "Command pm-disable needs a higher bootstrap level to run"?
This generally means that drush can't identify the site information, e.g. which settings.php to use.

A quick fix is to cd into the directory with the setting.php file for the site.

A more permanent fix is to create a site specific drush alias for the site and use it.  E.g. drush @mysite dis varnish. See this Drupal page.