After building a national reputation in the United States through his shipbuilding successes during the War of 1812, he became a prominent business and political figure in New York City in the 1810s, 1820s, and early 1830s.

The family soon moved to nearby Irvine, where he attended school and became a lifelong friend of schoolmate John Galt, a future novelist.

When Black moved to Kingston, Upper Canada on Lake Ontario late in 1792, Eckford followed to continue his apprenticeship, but the two soon went their separate ways, with Black moving back to Quebec City to pursue revolutionary politics (and also a shipyard in Lower Town from Ralph Gray) while Eckford stayed behind in Kingston to continue to learn the shipbuilding trade.

Around 1802, he sold his yard and moved back across the river to New York City, where he and Edward or Lester Beebe (sources differ)[10] opened a new shipyard together.

[9] He joined the Society of Mechanics and Tradesmen of the City of New York and a Freemason lodge, where he met such prominent New Yorkers as Mayor DeWitt Clinton, Governor Daniel Tompkins, Chancellor Robert Livingston, and John Jacob Astor, with whom he formed a lasting business partnership.

In July 1808, Christian Bergh invited Eckford to join him in building the 14-gun US Navy brig USS Oneida at Oswego, New York, on Lake Ontario.

Although he did not design Oneida, the project enhanced his reputation further with the US Navy and gave him experience in shipbuilding under the primitive conditions then prevailing along the New York shore of Lake Ontario.

[14] Returning to New York City in 1809, Eckford bought out his partner Beebe and became sole owner of a new shipyard he established which would remain his main place of business for the rest of his life.

[16][17] After the War of 1812 began in June 1812, Eckford offered his services to United States Secretary of the Navy Paul Hamilton in a letter of 8 July 1812.

Chauncey visited New York City in the first week of September 1812 to meet with Eckford and his fellow shipbuilders Christian Bergh and Adam and Noah Brown about the problem of building a fleet of warships on Lake Ontario.

Chauncey joined him at Sackets Harbor on 6 October 1812, establishing his headquarters there, and finding that Eckford already had a shipyard in operation and had laid the keel of the 42-gun frigate USS Madison.

[6][18] Despite terrible winter weather, Eckford not only quickly established a shipyard, but also quarters for the shipbuilders, mess and kitchen buildings, a hospital, offices, and blockhouses,[19] in what once had been merely a quiet hamlet, and made Sackets Harbor one of the US Navy's main bases during the war, also taking the opportunity to invest in real estate in the area.

Eckford understood that the American war effort on the Great Lakes required the US Navy to keep ahead of British shipbuilding in Canada, and that speedy construction and delivery of warships was critical.

[6][21] The Sackets Harbor yard also built smaller ships in record time; the schooner USS Sylph took only 21 days from keel-laying to launch in 1813.

[22] Eckford also demonstrated a facility for dealing with labour crises, as demonstrated by an incident on 1 May 1814, when a United States Army soldier on sentry duty at Sackets Harbor shot and killed a carpenter after the launching of USS Superior, provoking an armed confrontation between soldiers and shipyard workers, who threatened to go on strike and go home, crippling American shipbuilding on the Great Lakes; Eckford joined Chauncey and the US Army commander, Major General Jacob Brown, in talking to the men and defusing the situation, avoiding further violence and allowing shipyard work to continue.

"[26] In the words of maritime historian Howard I. Chapelle, "It was Eckford's extraordinary ability to design, lay down, and build ships, ranging in size from a very small schooner to the largest frigates, working in a wilderness and in severe winter weather with sick or dissatisfied labor, and to do all this in extremely short periods of time, that maintained American superiority on Lake Ontario.

"[27] Chapelle continues, "From a naval shipbuilding point of view, the outstanding men of the War of 1812 were Eckford and the Browns, Adam and Noah.

[30] In 1817, the Brooklyn Navy Yard laid down the largely Eckford-designed 74-gun frigate USS Ohio; she was launched in 1820 and established a model upon which "74s" were built thereafter.

Tradition holds that the ship also ran afoul of naval politics; it has been claimed that the Board of Navy Commissioners, led by Commodore John Rodgers, felt that Eckford had ignored their design for Ohio and blocked her completion.

[11] Eckford's family moved in New York City's higher social circles, and he expanded his business interests, including ventures in the shipping, banking, insurance, and publishing sectors.

On 15 September 1826, he and other Tammany Hall leaders were indicted for committing millions of dollars in acts of fraud against banks, insurance companies, and private citizens.

His oldest child Sarah, widowed when Joseph Rodman Drake suddenly died of consumption in 1820, fell ill in the autumn of 1827.

Eckford was part of this trend; in 1830, for example, he built the sloop-of-war Kensington in Philadelphia, Pennsylvania, for the Imperial Russian Navy, although ultimately the ship was delivered to Mexico instead.

Eckford, seeking to rebuild his fortune and reputation after the scandals of 1826 and 1827, left New York in June 1831[38] aboard the new 1,000-ton, 26-gun corvette United States, which his yard had built on speculation in 1830–1831[39] and which he hoped to sell to the Ottomans.