Answered User specific settings programatcally.

$user->getSettings();

/* Get the raw value of the user setting */
$userId = 12;
$settingKey = 'some_setting';
$newValue = 'someValue';

$fields = array(
    'user' => $userId,
    'key' => $settingKey,
}

$userSetting = $modx->getObject('modUserSetting', $fields);
if ($userSetting) {
    $settingValue = $userSetting->get('value');

    /* Put a new value in the setting */
    $userSetting->set('value', $newValue);
    $userSetting->save();
}

/* Get the raw value of the user setting */
$userId = 12;
$settingKey = 'some_setting';

$query = $modx->newQuery('modUserSetting', array(
    'user' => $userId,
    'key' => $settingKey,
));
$query->select('value');
$settingValue = $modx->getValue($query->prepare());