I would go with CLT given that it’s more compact in a pinch. if you haven’t already done so, check the typical on-time performance for the first leg as that should influence the decision. Gate staff at both hubs move quickly to offload planes.

I’d also look at which option provides a better connection in Boston to get from B to E. Depending on when you’re taking this trip, the runway construction happening here through November is typically resulting in EDCT times depending on the time of day and flow. Padding has been added to schedules, but my recent delays have been in excess of that padding.