I have used the boolean modifier to cut windows into this wall. However, it seems to have resulted in messy geometry. What would be the most efficient way to clean it up?
You could do it this way, and by the way you could have done it without booleans. Use the knife tool (K to activate, C to cut orthogonally, Z to cut through, E to continue, Enter to validate). To delete the bad edges, select them and X > Dissolve Edges.
You could try to simplify, actually it all depends on what you're planning to do later, but as Gorgious says you'll need to keep some edges between your holes and the external edges: