Came across these and thought people might find them interesting. These are the biggest cities in the British Isles in the 16th and 17th centuries, and some major towns, yet the populations are tiny. So it's perfectly possible to have a fantasy city with only a couple of thousand or so residents.
Aberdeen - 2,900 in late 16th century
Brighton - Less than 1,000 in 1520
Bristol - 12,000 in 1600
Canterbury - 6,000 by 1650
Chester - 7,600 in 1660s
Colchester - 9,000 in 1650s
Coventry - 6,000 in 1600
Dublin - 5,500 in 1600
Edinburgh - 9,000 in late 16th century
Exeter - 9,000 in 1603
Glasgow - 4,500 in late 16th century
Gloucester - 4,000 in 1563
Ipswich - 5,000 in 1600
Leicester - 3,500 in 1603
Manchester - 2,000 in 16th century
Newcastle-upon-Tyne - 12,550 in 1660s
Norwich - 15,000 in 1603
Portsmouth - 1,000 in 1600
Shrewsbury - 4,000 in 16th century
Winchester - 3,000 in 1603
Worcester - 8,300 in 1646
York - 11,000 in 1603
And now for the outlier:
London 200-250,000 in 1600
London is possibly a bad example; there aren't many cities where such a large percentage of the country's population resides within its metropolitan area (some city-states, a few others maybe), and the situation only got more extreme - close to 25% of the UK now lives within the London metropolitan area. Back then, it was about half the population of Scotland; now, it's substantially greater.