The blue, white and orange refer to the colors of the historical Dutch flag. Orange is the color the Dutch adopted after their leader William of Orange. The Committee's report stated that "the order of arrangement follows the practice found in the French, Belgian and other tri-colors, of placing the darkest bar next to the staff."
The New-York Historical Society originally proposed adopting a horizontal tricolor to be more reflective of the historical Dutch flags, but the Committee kept the vertical orientation.
Bald eagle: The symbol of the United States of America
Native American: The original inhabitants of the area
Seaman: Symbolizes the colonizers of the area
Beaver: Symbolizes the Dutch West India Company, which was the first company in New York (originally known as Nieuw Amsterdam). Also the official animal of New York State.
Windmill: Remembers the Dutch history of the city and the prosperous industry of milling flour.
Flour barrels: In the 17th century, New York had been granted a short-lived monopoly on milling, which established the fledgling colony as a commercial powerhouse
1625: Originally 1664, the year was later changed to honor the establishment of New Amsterdam, which was actually settled in 1624. The 1625 date has been described as "arbitrary" by the public historian at the New-York Historical Society and "simply wrong" by Michael Miscione, the Manhattan borough historian.