The Great Organ of Saint Thomas Church was built in 1913 by the Ernest M. Skinner Organ Company of Boston, and installed when the present building was first used for services that year. It was extensively revised and rebuilt in 1956 by the Aeolian-Skinner Organ Company, also of Boston, under the personal direction of G. Donald Harrison. It was then dedicated as the Arents Memorial Organ, given by George Arents in memory of his wife. Further revision of the instrument was completed in the late sixties by Gilbert Adams of New York, and in the early eighties by Mann and Trupiano of Brooklyn.
The current organ includes tonal designs which are characteristic of the organs of Bach's time. In addition, it is especially notable for its French Romantic colors. Consisting of six divisions, the instrument features a Trompette-en-Chamade under the rose window over the Fifth Avenue entrance. The organ console is hidden from view at the left of the chancel.
In the spring of 1996 the gallery instrument was dedicated as the Loening-Hancock Organ. The firm of Taylor & Boody of Staunton, Virginia built the instrument which contains twenty-one stops over two manuals and a pedal. The instrument is inspried by the tradition of organ building which was active in the Netherlands and North Germany in the seventeenth and eighteenth centuries. Stop and key action are mechanical and the temperament is Kellner.
The Martha J. Dodge Continuo Organ was built and initiated in December, 2001. This superb portative instrument, consisting of 4 ranks and pipes, was built by the firm of Taylor & Boody.