Sorry, there has been no statistics found for the percentage of individuals who can raise can both eyebrows independently.
Virtually everyone can raise both eyebrows, but only a portion of the population can raise one at a time – that is, without moving the other at all. Even the aforemetioned "portion" has not been converted into numbers.
When it comes to this kind data collection, we often use the words few or "a portion" (as mentioned above) in relating to the rarity of people who can actually do this.
There's a lot of quirky things we can do with our bodies--some things only a small percentage of us can do.
Dr. Kristin Woodward, an anesthesiologist who practices in Denver, Colorado, has studied this topic. Here's a compilation of list of rare body quirks, featured on Glamour.com.