As mentioned in the article, the “largest and costliest organ in the United States” belonged to Frederick G. Bourne’s and was installed in his Oakdale, Long Island home.
According to the Organ Historical Society’s Pipe Organ Database (who knew?) the residence became a military academy after Bourne died, and in 1948 the organ was sold. Part of it went to Detroit, and part went to San Diego.
Today, the largest organ in the United States may be (and I say “may” because I found conflicting details) the Wanamaker Organ currently displayed in a Macy’s Department store in Philadelphia.
RICH MEN WHO HAVE ORGANS BUILT IN THEIR HOMES: And Who Employ Organists by the Year to Give Them Music at Their Own Firesides — More Than $50,000 Has Been Paid for Some of These Organs. (PDF)
From September 17, 1911