Mooney enrolled in the Academy school's antique class in 1835; at the close of that year's season he was awarded the first prize, an inscribed, gold-washed miniature palette, in the competition for the best original drawing of a single figure. Academy classes were held in the evenings, and during the days Mooney supported himself by working as a sign and ornament painter, and by copying portraits by other artists. In about 1837 he entered the studio of Henry Inman. Mooney possibly remained his assistant for the remaining nine years of Inman's life, and certainly benefited greatly from the guidance of New York's foremost portraitist. He again enrolled in the Academy school, both antique and life classes for the 1838-39 season and for the life class only, 1839-40.
Mooney first exhibited in an Academy annual in 1838, and continued to be represented in these shows, hardly missing a year through 1874. The Academy exhibitions were virtually the only venue he used to display his work. Of the ninety-two paintings he exhibited in annuals over his working lifetime only two were not conventional portrait likenesses: Return From a Walk, presumably a genre subject, shown in 1840; and Armenian in Old Style of Turkish Costume, shown in 1849.
From the exhibition of his portrait of "Achmet Ben Aman" in the Academy annual of 1841, Mooney's career as a portraitist advanced steadily. His eulogy entered into Academy minutes took special note of his portraits of the New York mayors ordered for the City Hall collection, and of his large-scaled portrait of Governor William Seward, in the Albany state capital. Mooney executed approximately twenty portraits of faculty for Princeton University, earning him a particular identification with that school. While his career was essentially confined to New York, in its later years he several times passed his winters working in Columbus and Savannah Georgia. After 1874 he retired to his country home in Upper Red Hook.
In her lifetime his daughter, Ella, established the Mooney Traveling Scholarship in her father's memory, which around the turn of the century began to afford selected students of the Academy school the opportunity of two years' study abroad. She also gave the Academy Mooney's gold palette award, and in her will directed a number of paintings be presented to its collection.
