First, a cronjob (does not matter if you use ispconfig) has always to contain full paths, so it always have to start with "/usr/bin/php", so you have to enter in ISPConfig:
To use the php binary (which is outside of the web root), you have to ensure that you create it as full cron and not jailed cron.
But my recommendation is something else, as the cron.php file is in the web directory, the easiest and secure way to set this up is a url cron. For a url cron, you just put the url to this script in the cron command line in ispconfig. e.g.:
and ispconfig will create a cronjon that calls this url.