I’m assuming your referring to a server based cron job. I’m not sure if your familiar with it but you could also use WP Cron. It’s an api that built into core. It’s a little easier to work with than a true cron job IMHO. It does have a mild caveat however. Which could also be it’s strength.
The scheduled events do not fire based on the servers internal clock alone. A user or a visitor of some sort needs to visit the site before any scheduled events are fired.
After the user / visitor visits WP Cron checks it’s timers and fires the ones that are due.
You could use this to your advantage in your phpunit tests. This could become even a more viable solution if you’re also using a headless browser such as selenium web driver http://docs.seleniumhq.org/ to test front end functionality as well as the backend.