1.  John B. Linn & William H. Egle, eds.  1880. Record of Pennsylvania Marriages Prior to 1810.  Pennsylvania Archives, 2nd Ser.  Lane S. Hart, State Printer, Harrisburg, PA (online at GenealogyLibrary.com). Vol. IX, p. 256:

Marriages Authorized by the Buckingham Monthly Meeting of Friends. 1730--1810. Buckingham Monthly Meeting...
11, 11, 1801	Ely, John, Jr., and Rachel Hartley.

Back then, "Jr." did not necessarily indicate a father-son relationship.  It was used in the sense of "John, the younger," as opposed to "John, the elder," when two John's lived in the same community.

2.  Reuben P. Ely, Warren S. Ely, and Daniel B. Ely.  1910. An Historical Narrative of the Ely, Revell, and Stacye Families.  Fleming H. Revell, Co., New York (online at GenealogyLibrary.com).

p. 253

(142) JOHN ELY, son of Hugh and Elizabeth (Wilson) Ely, born March 9, 1778; died July 28, 1826; married, November 11, 1801, Rachel Hartley, daughter of Anthony Hartley, of Buckingham. He inherited the farm in Solebury devised to his father, but sold it in 1822 and thereafter lived in Plumstead and Buckingham, Bucks County. They had four children:-- 492. Hannah Ely, born February 21, 1802; married Moses Fell at Plumstead Meeting, August 15, 1822. He was born April 8, 1797, and died March

p. 254

31, 1887, and she died February 26, 1890. They had four children, viz:--   Annie E., born June 8, 1823; married, December 22, 1847, Isaac Saxton, and had one child, Walter G. Saxton.   Rachel, born June 9, 1825; married Mordecai Carman. She died without issue, in 1873.   John E., born April 1, 1827; married, first, Lydia S. Powell, and, second, her sister, (???) Powell; had four children.   Mary A., born February 24, 1830; married Zaccheus H. Powell, a Minister of the Society of Friends, and had four children.   Joseph S., died at the age of five years.   Elwood, born December 31, 1843; married Lovicy Aikins, and had seven children: Maud, Isabel, Annie, Mary, Howard Ely, Josephine and Louise. 493. David Ely, born August 29, 1803; died at the age of two weeks. 494. Elias Ely, born August 29, 1803; married Polly Landon, and had two children, John and David. 495. Hugh Ely, born April 27, 1805; married, first, Sarah Hustead, and, second, Clemanza Lawrence. Had one son by last marriage, viz:--   Irwin Ely.

3.  LDS.  Family Search: Internet Genealogy Service: Ancestral File.  The LDS AF has one John ELY as the son of both Hugh & Elizabeth (BLACKFAN) ELY and Hugh & Elizabeth (WILSON) ELY.  It also has this same John ELY as the husband of both Hannah AUSTIN and Rachel HARTLEY.  Elizabeth BLACKFAN is too old to be the mother of the John ELY born 1778 and the John ELY born in 1778 is too young to have children born in the 1770s/80s, so these must be two different John ELYs, the older one married to Hannah AUSTIN and the younger one married to Rachel HARTLEY (and so I later find — see next source):

Hugh ELY (1715-1791) = Elizabeth BLACKFAN (1718-1796) | John ELY (bef. 1760-?) = Hannah AUSTIN (bef. 1760-?)

Hugh ELY (1741-1805) = Elizabeth WILSON (1739-1821) | John ELY (1778-1826) = Rachel HARTLEY (1773-?)