What colonial city had the highest population in 1776?

The largest city in 1776 was Philadelphia, followed by New York and Boston.

http://economistsoutlook.blogs.realtor.org/2012/07/03/largest-cities-in-the-united-states-in-1776-and-in-2076/

At the time of the nation’s independence the total population in the U.S. was 2.5 million. Philadelphia was the largest city with 40,000 residents – which would only fill about half the capacity at Lincoln Financial Field where its football team plays home games today. The Quaker-populated city back then was very peaceful and civil, very unlike the Eagle fans of today. In 1776, the next largest cities were New York City (25,000 people), Boston (15,000), Charleston (12,000), and Newport (11,000). All are rough estimates as the U.S. Census enumeration did not begin until the 1790.