The Port of Northport lies on the northern shores of Long Island, connected to Long Island Sound by the Northport and Huntington Bays. Sailing around Long Island, the Port of Northport is about 91 nautical miles from Bay Shore Harbor on south Long Island, but it is only 23 kilometers (14 miles) north-northwest of Bay Shore Harbor by land. The Port of Northport is about 50 nautical miles (70 kilometers or 43 miles) east-northeast of the Port of New York. The 2010 US Census reported that just over 7400 people lived in the Port of Northport.
The Matinecock ("at the hilly land") people lived in area that would become the Port of Northport long before Europeans arrived, their lands stretching from today's Queens to Suffolk County and Long Island. The Matinecocks were generally peaceful with the European settlers, but hostilities occurred now and then.
In 1639, the chief sachem signed a deed conveying the western half of Long Island to Dutch settlers. Unfortunately, the settlers assumed the deed gave them all Matinecock lands. In the winter of 1643, the Dutch attacked a Matinecock village killing more than 120 men, women, and children.
Continued immigration of European settlers to the future Port of Northport through the 1650s led to troubles for the Matinecock people. English settlers brought livestock that overran the Matinecock's unfenced lands, and they introduced liquor into their trade that led to tribal disorganization and demoralization. By 1650, many Matinecock had died from European diseases and fighting with the Dutch and other tribal enemies.
New Netherland fell into British hands in 1664, and the settlers living what would become the Port of Northport pushed for the Matinecock to be evicted. The settlers continued to drag the people into court, and the last parcels of the Matinecock's land were sold in 1676. By 1685, all disputed Matinecock lands were in the hands of the settlers.
With their lands gone, many Matinecock joined other tribes. Some that stayed on their ancestral lands became British plantation workers. Many Matinecock became harpooners and played an important role in the development of the Long Island whaling industry. By the early 1730s, the Matinecock villages on western Long Island had disappeared.
Known at the time as Opcathontyche, three Englishmen bought the land for the Port of Northport from the Matinecock in 1656. By the early 1800s, farmers settled the land around the harbor, resulting in the area's nickname as Great Cow Harbor. The 1761 Skidmore House on the Port of Northport's Main Street is the oldest standing home in the Port of Northport.
In the late 1830s, the Port of Northport got its current name when there were eight dwellings in the village. The shipbuilding industry brought growth and change to the Port of Northport, and it soon became the town's major industry.
By 1860, over one thousand people called the Port of Northport home. By 1874, it was the fastest-growing town on the north shore. The Port of Northport had three ship yards, two hotels, six general stores, and five sets of marine railways. The shipbuilding boom lasted for half a century until steel-hulled ships began to replace the wooden vessels constructed in the Port of Northport.
In 1868, a Long Island Railroad station was opened in the Port of Northport to accommodate the town's growing population of commuters. The station operated for a few years until the railroad moved it to a new Larkfield Road station. The original rails to the Port of Northport became known as the Northport Branch, and Larkfield was called East Northport.
When the railroad was moved and the station closed in 1899, the Port of Northport built a 2-1/2 mile trolley line to move commuters from Main Street to the new rail station in Larkfield. The trolley made commuter runs until 1924 when the newly-introduced automobile made it obsolete.
Over the years, the Port of Northport has expanded and annexed surrounding communities including the settlement of Crab Meadow and parts of the Freshpond community.