What is the largest plane ever to have been stolen by a single pilot?
Probably the one you stated in your question.  Though, I should note, that there is some credible evidence that only one person was actually flying the plane and the other may have been forced into coming along.  So you could probably consider it to have been stolen by one person, and that person appears to have not been remotely qualified to fly it.  When it was leaving the plane seemed to meander down the taxiway to the runway, like the pilot had no idea what they were doing, and then it took off.  It hasn't been seen since, and most credible theories think it crashed in the ocean.  But conspiracy theories abound.

A close second would probably be this ATR-42-320(wikipedia plane reference), also stolen in Africa.  This time by an employee of the company who was, unfortunately, suicidal.  He flew the plane around the airport for a few minutes demanding to speak to everyone from his boss, to his significant other to the president of the country.  He eventually crashed it into a couple of other ATR's the company owned.

In reference to the "I'm writing a story" line.  I would suggest that a 727 probably isn't the optimal plane for a single person to steal.  They're older and difficult to manage on your own.  I think a much better option would be a more modern aircraft, like an Airbus A350 or a Boeing 787.  They have avionics that allow for one person to reasonably fly the plane.  

Granted, they are very new and may be harder to steal.  Probably the sweet spot between "new enough to be flyable by one person" and "old enough to have one just sitting around to be stolen" would be something like a 737-800 or an Airbus A320.  Both are still quite large, but a skilled pilot could probably operate one on their own if they needed to.  In fact, it has happened before.