Run PhpUnit from wihtin PhpStorm through vagrant on virtual machine. Use this file as Custom Loader. See http://www.jetbrains.com/phpstorm/webhelp/phpunit.html

PhpStormVagrantPhpUnit.php

<?php

/** Full path to project dir on host */
isset($_SERVER['HOST_DIR']) or $_SERVER['HOST_DIR'] = realpath(__DIR__ . '/../../');

/** Full path to vagrant directory on host */
$_SERVER['VAGRANT_DIR'] = $_SERVER['HOST_DIR'] . '/vagrant';

/** Full path to project dir on virtual machine */
$_SERVER['GUEST_DIR'] = '/path/to/project/on/vm';

/** Full path to phpunit binary on virtual machine */
$_SERVER['TEST_RUNNER'] = $_SERVER['GUEST_DIR'] . '/vendor/bin/phpunit';


if (!in_array($_SERVER['PHP_SELF'], array('-', $_SERVER['TEST_RUNNER']))) {
    $exit = 0;

    $map = function ($string) {
        return str_replace($_SERVER['HOST_DIR'], $_SERVER['GUEST_DIR'], $string);
    };

    $arg = array_map('escapeshellarg', $_SERVER['argv']);
    $arg = array_map($map, $arg);

    array_splice($arg, 0, 1, array(
        'cd', escapeshellarg($map(__DIR__)), '&&',
        'HOST_DIR=' . escapeshellarg($_SERVER['HOST_DIR']),
        escapeshellarg($_SERVER['TEST_RUNNER']),
        '--printer', 'PhpStormVagrantPhpUnit'
    ));

    $cmd = escapeshellarg(join(' ', $arg));

    chdir($_SERVER['VAGRANT_DIR']);
    passthru("vagrant ssh -c $cmd", $exit);

    exit($exit);
}

class PhpStormVagrantPhpUnit extends PHPUnit_TextUI_ResultPrinter implements PHPUnit_Framework_TestListener
{
    private $isSummaryTestCountPrinted = false;

    /** @var PHPUnit_Util_Printer $printer */
    private $printer = false;

    /**
     * @param PHPUnit_Util_Printer $printer
     */
    function __construct($printer)
    {
        $this->printer = $printer;
    }

    protected function writeProgress($progress)
    {
        //ignore
    }

    public function printResult(PHPUnit_Framework_TestResult $result)
    {
        $this->printHeader();
        $this->printFooter($result);
    }

    /**
     * @param  string $buffer
     */
    public function write($buffer)
    {
        print str_replace($_SERVER['GUEST_DIR'], $_SERVER['HOST_DIR'], $buffer);

        if ($this->autoFlush) {
            $this->incrementalFlush();
        }
    }

    private function printEvent($eventName, $params = array())
    {
        $this->printText("\n##teamcity[$eventName");
        foreach ($params as $key => $value) {
            $this->printText(" $key='$value'");
        }
        $this->printText("]\n");
    }

    private function printText($text)
    {
        $this->write($text);
    }

    private static function getMessage(Exception $e)
    {
        $message = "";
        if (strlen(get_class($e)) != 0) {
            $message = $message . get_class($e);
        }
        if (strlen($message) != 0 && strlen($e->getMessage()) != 0) {
            $message = $message . " : ";
        }
        $message = $message . $e->getMessage();
        return self::escapeValue($message);
    }

    private static function getDetails(Exception $e)
    {
        return self::escapeValue($e->getTraceAsString());
    }

    private static function getValueAsString($value)
    {
        if (is_null($value)) {
            return "null";
        } else if (is_bool($value)) {
            return $value == true ? "true" : "false";
        } else if (is_array($value) || is_string($value)) {
            $valueAsString = print_r($value, true);
            if (strlen($valueAsString) > 10000) {
                return null;
            }
            return $valueAsString;
        } else if (is_scalar($value)) {
            return print_r($value, true);
        }
        return null;
    }

    private static function escapeValue($text)
    {
        $text = str_replace("|", "||", $text);
        $text = str_replace("'", "|'", $text);
        $text = str_replace("\n", "|n", $text);
        $text = str_replace("\r", "|r", $text);
        $text = str_replace("]", "|]", $text);
        return $text;
    }

    private static function getFileName($className)
    {
        $reflectionClass = new ReflectionClass($className);
        $fileName = $reflectionClass->getFileName();
        return $fileName;
    }

    public function addError(PHPUnit_Framework_Test $test, Exception $e, $time)
    {
        $this->printEvent("testFailed", array(
            "name" => $test->getName(),
            "message" => self::getMessage($e),
            "details" => self::getDetails($e)
        ));
    }

    public function addFailure(PHPUnit_Framework_Test $test, PHPUnit_Framework_AssertionFailedError $e, $time)
    {
        $params = array(
            "name" => $test->getName(),
            "message" => self::getMessage($e),
            "details" => self::getDetails($e)
        );
        if ($e instanceof PHPUnit_Framework_ExpectationFailedException) {
            $comparisonFailure = $e->getComparisonFailure();
            if ($comparisonFailure instanceof PHPUnit_Framework_ComparisonFailure) {
                $actualResult = $comparisonFailure->getActual();
                $expectedResult = $comparisonFailure->getExpected();
                $actualString = self::getValueAsString($actualResult);
                $expectedString = self::getValueAsString($expectedResult);
                if (!is_null($actualString) && !is_null($expectedString)) {
                    $params['actual'] = self::escapeValue($actualString);
                    $params['expected'] = self::escapeValue($expectedString);
                }
            }
        }
        $this->printEvent("testFailed", $params);
    }

    public function addIncompleteTest(PHPUnit_Framework_Test $test, Exception $e, $time)
    {
        $this->printEvent("testIgnored", array(
            "name" => $test->getName(),
            "message" => self::getMessage($e),
            "details" => self::getDetails($e)
        ));
    }

    public function addSkippedTest(PHPUnit_Framework_Test $test, Exception $e, $time)
    {
        $this->printEvent("testIgnored", array(
            "name" => $test->getName(),
            "message" => self::getMessage($e),
            "details" => self::getDetails($e)
        ));
    }

    public function startTest(PHPUnit_Framework_Test $test)
    {
        $testName = $test->getName();
        $params = array(
            "name" => $testName
        );
        if ($test instanceof PHPUnit_Framework_TestCase) {
            $className = get_class($test);
            $fileName = self::getFileName($className);
            $params['locationHint'] = "php_qn://$fileName::\\$className::$testName";
        }
        $this->printEvent("testStarted", $params);
    }

    public function endTest(PHPUnit_Framework_Test $test, $time)
    {
        if ($test instanceof PHPUnit_Framework_TestCase) {
            $this->numAssertions += $test->getNumAssertions();
        }
        else if ($test instanceof PHPUnit_Extensions_PhptTestCase) {
            $this->numAssertions++;
        }
        $this->printEvent("testFinished", array(
            "name" => $test->getName(),
            "duration" => (int)(round($time, 2) * 1000)
        ));
    }

    public function startTestSuite(PHPUnit_Framework_TestSuite $suite)
    {
        if (!$this->isSummaryTestCountPrinted) {
            $this->isSummaryTestCountPrinted = true;
            //print tests count
            $this->printEvent("testCount", array(
                "count" => count($suite)
            ));
        }

        $suiteName = $suite->getName();
        if (empty($suiteName)) {
            return;
        }
        $params = array(
            "name" => $suiteName,
        );
        if (class_exists($suiteName, false)) {
            $fileName = self::getFileName($suiteName);
            $params['locationHint'] = "php_qn://$fileName::\\$suiteName";
        }
        $this->printEvent("testSuiteStarted", $params);
    }

    public function endTestSuite(PHPUnit_Framework_TestSuite $suite)
    {
        $suiteName = $suite->getName();
        if (empty($suiteName)) {
            return;
        }
        $this->printEvent("testSuiteFinished",
            array(
                "name" => $suite->getName()
            ));
    }
}

This is excellent. One thing that helped me figure this out was to realize that this is not meant to aid "PHPUnit On Server" tests, but to trick the normal PHPUnit testing to use the correct stuff.

It was also helpful to install the vagrant-phpstorm-tunnel plugin for vagrant, as well. More info about it can be found at https://github.com/cargomedia/vagrant-phpstorm-tunnel