I rate them as equal in taste, so I would use another characteristic to make the choice. The following observations are based off of comparing the standard black Jaboticaba and the Ison muscadine (a self fertile variety).
Advantages of jaboticaba include lower maintenance (does not need pruned each winter), longer fruiting season (due to potential for multiple crops), and self fertility (the very best muscadines need a polenator).
Advantages of muscadines include greater cold tollerence (no need to cold protect in 9b EVER), better adaptation to drought once established, firmer texture of fruit pulp, ability to be trained in linear spaces that would otherwise be wasted (like on a fence), greater ease of vegetative propagation, and a shorter time to come into full production.
One last thing that I will mention is that muscadine peels can make my mouth itch when I eat large amounts of fruit. I think this is a very mild allergic reaction and no one else in my family gets it. I have never had that reaction with Jaboticaba.