He was likely born about 1644/5 at England or Southold, Suffolk County, New York, as he was of full age when a vote was held on 20 January 1665/6: 
At a Towne meting held the 20th of Jan. 1665, granted vnto John Whitne the sonne of Henry Whitney ... oinse unto his father's home lott extending from the ... Brow of the hill lying by the hi ... weight Leading to the ... 2 Rodds ... cartpath by the sayd Falls.
He was a millwright and miller after his father.  He inherited his father's cornmill as well as the homestead. 
A fulling mill from 1661.
At a towne meting desember 27th 1677. At ye aforesayd meting it was voted and agreed on between the towne and the miller, John Whitne, that the towns men are to carry their corne to the mill vpon the third and sixt dayes of the weak, comonly called Tuesday & Fryday, which days he is to Attend to grinde in & if the sayd John can clere the mill of the corne that is brought in the aforsayd two days, or before, then the Rest of the dayes of ye week he may take to atned his own ocations, but if he cannot clere the mill of the corne sesonably brought in he must clere it before he leaues.
Beside the cornmill, he built a fulling mill. These were for cleaning either cloth or the cotton they were made with. The contraption was hooked up to a watermill. 
↑ 2.02.12.22.32.4 Stephen Whitney Phoenix, The Whitney Family of Connecticut and its Affiliations; Being An Attempt to Trace the Descendants, as well in the Female as the Male Lines, or Henry Whitney, from 1649 to 1878, To Which is Prefixed Some Account of the Whitneys of England, New York: Privately Printed, 1878. Ancestry.com. (The Whitney family of Connecticut, and its affiliations [online database], Provo, Utah: Ancestry.com Operations, Inc., 2005), pg. 11.
He settled, with his father, in Norwalk, followed his business, of millwright, and miller; succeeded him in the possession of the mill and homestead; and married 17 Mar 1674/75, Elizabeth SMITH, dau. of Richard Smith. [Phoenix p11]
'Whitney, John, Norwalk, only son of Henry, married 17 Mar 1675, Elizabeth, daughter of Richard SMITH, probably of L.I .
Had John born 12 Mar 1677;
Joseph, 1 Mar 1679,
Henry, 21 February 1681;
Richard, 18 Apr 1687
but no more known of him except that he was a miller, had good property and his children perpetuated the name in that region.' [Savage p530]
Savage was INCORRECT in listing a child of John and Elizabeth (SMITH) WHITNEY. John and Elizabeth did NOT have a child named Samuel. This error was repeated in various publications, including several Connecticut town histories and the books by S. Whitney Phoenix. 'Saml. WHITNEY of Stratford' (who married Anne LABOREE) was the son of Nathaniel WHITNEY and Sarah HAGAR - and thus a descendant of John and Elinor WHITNEY of Watertown. Proof lies in the probate records of Samuel's father, Nathaniel WHITNEY, Middlesex County, MA, File No. 24731.
He died before November 1720 in Norwalk, Fairfield, Ct. He was married to Elizabeth Smith (daughter of Richard Smith and Bathsheba Rogers) on March 17, 1673/74 in Norwalk, Fairfield, Ct. Elizabeth Smith was born about 1650 in Norwalk, Fairfield, Ct. She died after April 3, 1741 in Ct.
It may be possible to confirm family relationships with John by comparing test results with other carriers of his Y-chromosome or his mother's mitochondrial DNA.
However, there are no known yDNA or mtDNA test-takers in his direct paternal or maternal line.
It is likely that these autosomal DNA test-takers will share DNA with John: