The original scream was an electron disruption field that ****ed matter up, releasing a lot of energy. Control over it was tied to the speech center of his brain. Given the nature of the power it's conceivable magneto could counter it and create a 'silence' zone around himself within the shield. This sonic version sucks.
Black bolt also struggled with fine control for a good portion of his career and depended on that antenna in his head for stable use of his powers. I haven't seen that being referenced in a while so he propbably got over it, but that would be a good weakness for magneto to exploit.
Regardless, magneto woud give him a very tough fight and I think he could take a majority through finer control and a mostly equal raw power - excluding the scream's hype.
If black bolt is in a situtaion where he is unlikely to use the scream to avoid collateral damage, then mags has a clear edge.