Henry's well known younger brother was the financier William Collins Whitney (1841–1904), who served as Secretary of the Navy in the first administration (1885–1889) of President Grover Cleveland.

[2] His sister Lucy Collins "Lily" Whitney married Charles T. Barney, who became the president of the Knickerbocker Trust Company.

[8] Upon his father's death on October 24, 1878, Whitney was elected his successor as president of the Metropolitan Steamship Company, retaining the position of agent at Boston.

[8] In June 1890 the Metropolitan Steamship Company placed the new iron steamer H.M. Whitney in service between Boston and New York.

By the next year it had consolidated ownership of a number of horse-drawn streetcar lines, composing a fleet of 7,816 horses and 1,480 rail vehicles.

A section of track was used to test the Bentley-Knight underground power line, but it was abandoned because of failures and safety concerns (especially after the electrocution of a team of horses in 1889).

After competing in operational tests with the Sprague streetcar system, the Thomson-Houston company was chosen for system-wide deployment of overhead wires.

[18][failed verification] The group purchased one coal mine and obtained options on others south of Sydney in eastern Cape Breton Island.

The Whitney syndicate was offered an unprecedented 99-year lease at a fixed royalty; the group exercised its options, acquiring most of the existing bituminous coal mines of eastern Cape Breton Island and co-opting such local figures as John Stewart McLennan and David MacKeen.

There were, however, costly mistakes, prominent among them the tendency to become locked into low-price contracts (such as to Whitney's companies), thus missing a large market at higher prices.

The company made a large public offering of stock, which tumbled in price when Whitney failed to get the American import duty on coal removed or at least reduced.

[23] Whitney expanded operations at Sydney with the organization in March 1899 of the Dominion Iron and Steel Company Ltd. (DISCO), which had financial backing in both Canada and the United States.

The promise of federal bounties, together with concessions from the Liberal provincial administration of Premier George Henry Murray, enabled DISCO to begin work in June 1899 on the largest integrated steel mill in the British Empire.

[28] In 1905, Whitney ran for Lieutenant Governor of Massachusetts as a Democrat, losing by 1,996 votes to Republican Eben S. Draper, which prompted a recount.

[32] MacFarland felt that Whitney represented corporate interests over "true Democratic principles"[32] in his support of the merger of New York, New Haven and Hartford with Boston and Maine railroads.

[32] Whitney eventually failed in his bid to unseat the Republican incumbent, Curtis Guild Jr. Eleven days later, he represented the family, along with Harry Payne Whitney, at the funeral in New York City of his brother-in-law, Charles T. Barney, who had shot himself following the failure of the Knickerbocker Trust Company in the Panic of 1907.

Largely because of the easy success of his younger brother, Whitney was generally supposed to be wealthy, but he had suffered losses from poor investments over a period of years.