There are several statements made in various comics (in several continuities) that support the idea of Supergirl being potentially the stronger of the two. Most notably, in the 2005-2011 run of Supergirl, Batman notes that she metabolizes solar energy more efficiently than Superman, leading him to theorize that she may be more powerful. There are other examples too, especially in the New 52 continuity. That being said, these answers ultimately come down to the whims of whomever is writing the story at the time, be it for comics or television. If a particular writer says Supergirl is stronger in their continuity, that's how it is. If the next writer decides to tow the more conventional line that Superman is the strongest superhero, then that becomes true again. I really don't think there's an objective standard here.
