Ok so the problem was I wasn't passing in the configuration file to PHPStorm. Once I did that through the 'edit configurations' dialog, I could see this in the console
vagrant:///Users/amiterandole/PhpstormProjects/flyer/usr/bin/php /home/vagrant/.phpstorm_helpers/phpunit.php --configuration /vagrant/phpunit.xml tests\integration\models\LikesTest /vagrant/tests/integration/models/LikesTest.php
and it worked!