"Greatest" brings to mind a trendsetter, a revolutionary, one that changed people's lives forever.
Although, the Comet was the first commercial jet, my personal choice as the greatest aircraft would be the Boeing 707.
This was an aircraft nobody was willing to bet on, but Boeing went ahead and put her in the air. This is the spirit that is missing in Aircraft manufacturers today, where the balance sheet is more important than foresight.
The B707 is what inspired the entire current generation of airliners, from the B737 to the A380. Unfortunately, without the Sonic Cruiser, it will be the way aircrafts look for a very long time to come.