The 1640's was a dangerous decade, a time of war when the Dutch colony at the foot of Manhattan could have been snuffed out. The director, Willem Kieft, who had been trying to tax the local Lenapes (while clearing more land for farming) was outraged by their refusal to pay for their own protection.
In February of 1643, after a series of raids and retaliatory skirmishes, Kieft ordered a Dutch platoon to attack two unsuspecting villages late at night. They returned with 80 heads of men, women and children. The Year of Blood followed. Many small settlements were destroyed including Bloemendael (on the present-day Upper West Side) and one farther north (which would be resettled in 1658 and named Haarlem).
It was during this time that Anne Hutchinson and most of her family (expelled from Massachusetts and living in what is now the Bronx) were massacred. (According to an article in The New Yorker by Ian Frazier, one of the surviving children is the direct ancestor of three presidents--Franklin Delano Roosevelt and the Bushes. Who knew they were related?)
When the war ended, hundreds (as many as 1600) of Indians and scores of Dutch were dead. In 1645, Kieft was recalled to Holland to face an inquiry, but he died when his ship sank off the coast of Wales. He left behind a colony in shambles and one in serious need of reform.
The Dutch West India Company searched their ranks for a new director. In 1647, a ship arrived bearing Peter Stuyvesant, who would govern the colony with an iron fist and a wooden leg until the British takeover in the 1660's.
Seen in the diorama at the American Museum of Natural History (pictured), Stuyvesant quickly made peace with the local tribes (though he did retain the laws forbidding fornication with them) and he set to restoring order. He banned drinking on Sundays and imposed fines for missing church and for speeding along De Heere Straet (Broadway). He also waged war against all the household garbage tossed into the street and the roaming swine, cows, goats, and chickens which dined off it. In 1648, he instituted an animal pound and ordered his soldiers to shoot any pig rooting near the foundation of the fort.
But that was just the beginning. Stuyvesant would transform the town in the next decade after announcing to the population that he would govern them "as a father his children."
ALSO DURING THIS DECADE:
1641: To win support for his war on the local Indians, Kieft establishes a Council of Twelve to be elected by the people. This is the first popularly chosen body in the future state of New York. In 1642, Kieft strips this body of all authority when not only does it refuse to recommend the war but it starts advising him on other topics.
1643: Anabaptists (forerunners of Quakers), expelled from Massachusetts, settle Gravesend, Brooklyn, just north of Coney Island. They are chased off, perhaps by the same raiders who massacred Hutchinson's family, but return to Gravesend in 1645 once peace is restored. (English settlers also establish Hempstead and Flushing during this period.)
1648: The first pier is built on the East River at Schreyer's Hook.
Sources: Gotham by Edwin G. Burrows and Mike Wallace; Manhattan in Maps by Robert T. Augustyn and Paul E. Cohen; The Historical Atlas of New York City by Eric Homberger; New York: An Illustrated History by Ric Burns and James Sanders, with Lisa Ades; The Island at the Center of the World by Russell Shorto; and The Big Oyster by Mark Kurlansky.