The evidence based answer is that neither one is better than the other, although it’s not always a coin toss. Clinical circumstances dictate the choice of modalities. V/Q scanning might be preferable if the patient is at risk for contrast induced renal failure. In the evaluation of chest pain if cardiac catheterization is planned V/Q scanning may be preferable to avoid a double contrast load. If stress nuclear myocardial perfusion is planned CT may be preferable, since the nuclear medicine myocardial perfusion scan will have to be delayed following V/Q scanning. An abnormal chest xray or COPD lessens the likelihood of a diagnostic V/Q scan.
A recent concern is that, because nuclear medicine scanning is being abandoned in favor of CT, the radiologists may be losing their interpretive skills.