Billboard analyzed market share, revenue and other data to compile its list. The power couple have each founded their own companies, Roc Nation and Parkwood Entertainment.
The rapper's longtime associate, Lyor Cohen, came in at number 74 on the list. He told Billboard: "Artists have always had the power but courage is in short supply. It's just that the hip-hop generation believes in the possibilities. Jay and Beyonce don't listen to the noise - they make the noise."
Rounding out the top three are Lucian Grange, president of Universal Music Group, and Tim McGraw and Alicia Keys' manager Coran Capshaw.
The power couple will be performing at the Grammy Awards on Sunday night. It is unclear if they will appear on stage together, but they have recently collaborated on Beyonce's single, "Drunk in Love."
Beyonce's latest, self-titled, album had not yet been released when the nominations were announced. However, Jay Z's "Magna Carta... Holy Grail" album has been nominated in nine categories.