Secondary sources are all over the map with regard to the identity of John's wife — caveat emptor!

1.  Marriage Record:

2.  Robert B. Miller & Albert Brown Lyons, eds.  1907. Lyon Memorial III:  New York Families Descended from the Immigrant Thomas Lyon of Rye.  Self-published. [W. Graham Printing Co., Detroit, MI.]  539 pp.  (facsimile reprint available from Higginson Books; online at Ancestry.com; boldface mine):

p. 47	5. II. 1. JOHN2 LYON [Thomas1], born, probably at Fairfield, Conn., about 1655, and died in Greenwich in 1736.  He lived with his brother, Samuel on the undivided estate left by their father, Thomas Lyon.  The name of his wife has not been ascertained.  John Lyon was deputy to the General Court of Connecticut from Fairfield, Conn., 1725-1730.  Feb. 27, 1698-9, at a meeting of the proprietors of the town, it was agreed "that we doe impower the aforesaid men (Hecaliah Brown, Deliverance Brown, John Merritt, Robert Bloomer and John Stockham) to bargain with and sell unto John Lyon a certain tract of land lying up Byram river, if they shall see good and convenient soe to do," and to John Lyon was confirmed "a parcel of land lying against the mill between the cartway down into the Neck and the mill creek bounded up the said creek by John Hoit's meddow and to run down to the said Creek till it comes to John Boyd's meddow, provided the said John Lyon doe not praidice the carte way into the neck, nor the way to the mill, neither shall hee hinder any person from settin up thare field fence if they have occasion."  At a town meeting held Sept. 20, 1697, Cap Theall, John Horton, Joseph Purdy, Hecaliah brown, John Lyon, Thomas Merritt and Isaac denman were Chosen a committee "for the management and carrying on of the worke of building a meeting house for the towne of Ry, and also for the appointing of a place where it shall set, and the above meeting house shall not acsed above thirty square feet."  The seating space of this place of worship speaks for the size of the congregation, which doubtless comprised every family in the settlement.
	Thirty square feet?  Surely the writer meant thirty feet square.
	In April 1699, John Lyon and Isaac Denman were chosen to lay out a road to White Plains [Westchester Co., NY], "beginning at the head of Capt Theall's land and so to run to the caseaway (causeway) brook," said road to be three rods in breadth.  July 14, 1710, John Lyon signed a quit claim for
p. 48	all obligations due him from his brother Joseph; witnesses Richard Ogden and John Stockham.  Feb. 1714 ("one thousand seven hundred and thirteen fourteen") John Lyon, Sr., living at Byram in the Town of Greenwich, deeded to his son Daniel Lyon of the same place his dwelling house and home lot, with all his lands and meadows on "Byrum Neck" not already disposed of to his son John Lyon, Jr.; John Corbit witness.  His will (Stamford Probate rec. Lib. I, p. 115) was dated Jan. 24, 1736; executors John Merritt and Samuel Brown; witnesses Johannes Dow, David Lyon, George Gorham.  He bequethed to Caleb Lyon, son of his son Thomas, deceased, one half the mill in Greenwich, with one half the lands pertaining to it, he to pay to his sister, when he should come of age, £30 current money; Thomas, brother of Caleb to have the other half of the mill property; to his son John the western and to his son Daniel the eastern half of the land at Byram Neck already deeded to them, Daniel to have also the lands on "Mary's Hill."  (In case Daniel died leaving no male heir the lands bequeathed to him were to go to James Lyon son of John, Jr.)  The moveable estate to be divided equally between "my four daughters, Ruth, Mary, Hannah and Jude."  For full text of the will see appendix, note 8. Children of John Lyon:   *22.   I.   Thomas; b. before 1689; d. 1733; m. Rebecca Hobby.   *23.   II.   Daniel; b. about 1688; d. 1752; m. Sarah Jennings.   *24.   III.   John; b. about 1690; d. July 1749; m. Hannah, widow of Joseph Banks.   25.   IV.   Ruth; living in 1736.   26.   V.   Mary; living 1736.   *27.   VI.   Hannah; b. 1704; d. about 1790; m. _____ Close.   28.   VII.   Jude; living 1736.

3.  GEDCOM provided by descendant.