Here's the difference (I'm a huge Prince fan by the way)
Prince musically is on another level than MJ. He can play something ridiculous like 20 instruments, wrote hits for bands and artists you would be shocked to know. Had so many different genre's of music from pop, rock, R&B, classical, Soul and even country in some of his sounds.
Prince also has an amazing voice, his octave range is incredible.
He was a musical prodigy, he was playing the paino by ear at like age 3 or 4. We know what he can do with the guitar and Rolling Stone magazine named him top 30 greatest guitarist of all time and said he should have been higher but he didn't have the body of work in the rock genre.
MJ on the other hand was the ultimate performer. He was magic, there's no other way to say it. To those who were alive in the 80's and understand what MJ did for pop culture and music, there was nobody bigger than him.
He was an incredible dancer, performer and his voice was amazing. He also wrote a lot of his music, more than people give him credit for and even know about.
So I think as a pure musician, it's Prince.
As the greatest entertainer that we have ever seen, it's MJ.