cron.php error with joomla 3.4 uri.php
I had exactly this problem too and it seemed to me that the missing class should have been loaded earlier in the sequence. In Civi 4.6 there is an extra statement on line 646 of /home/[USERNAME]/public_html/info/administrator/components/com_civicrm/civicrm/CRM/Utils/System/Joomla.php so I made my 4.4.20 version look like this (with Joomla 3.4.5):

if( version_compare(JVERSION, '3.0', 'lt') ) {
  require $joomlaBase . '/libraries/joomla/environment/uri.php';
  require $joomlaBase . '/libraries/joomla/application/component/helper.php';
}
else {
  require $joomlaBase . '/libraries/cms.php';
  require $joomlaBase . '/libraries/joomla/uri/uri.php';
}


It is the require $joomlaBase . '/libraries/cms.php'; statement that I added.

I am not sending mail at the moment but at least the crons have stopped sending me error messages every 10 minutes. I could not upgrade to 4.6 so this will have to do for me for now.