What specific time period are you interested in?

The Byzantine Empire spans over a thousand years of history, with many changes in social and political structuring. Population centers often shifted from one century to the next. One cannot simply list the "most populous" cities and expect that list to remain unchanging and eternal.

All of the answers below, first, lack sources, and second, list locations that were not always parts of the Empire, save Constantinople (with the exception of 57 years between the formation of the Latin Empire and the retaking by the Palaiologoi). Alexandria was held for less than half of the Empire's history, as was Antioch (which was often contested), and both of these likely suffered mass depopulations during the Arab Invasions. The way I see it, to indicate these as the "largest population centers" of the Empire is rather false, since again, they were not held under Imperial control for a good portion of the Empire's history. There were other very large population centers that could be considered part of the "Imperial heartland" that are much better choices to examine - I'm surprised that nobody mentioned Thessalonika, for example, which then and now, was considered the "Second City" of the Empire.

After the conquest of Egypt by the Muslims, the Eastern Roman Empire lost its most populous province and most likely largest city at that point (Alexandria). After that Constantinople would be the largest city and the most productive region would either be Thrace or Western Anatolia (until they lost that as well)