Either one's fine. Nov-Apr is probably the best time to visit Tokyo weather-wise. Early-summer starts to get hot with more rain, July~Sept is very muggy, you can get typhoons from late summer through Oct.

You can expect the most sun, driest weather, and clearest sky in winter. Winter in Tokyo is not that bad... certainly far easier to bear than summer time. But as others have said, the cherry blossom in Mar~Apr will be a nice thing, plus it should be warmer.