One of the first to make this error was Alonzo Lewis in his "History of Lynn" (Boston: H.H. Eastburn, 1829) in which he states, "I have ascertained that he died at Hackney, in England, at the age of about one hundred years." (p.151) From there the error has continued to spread, until it has become impossible to put down. One can find several mentions of the 1660 Hackney death in many places in print and on the Internet.
One caveat on the date of death supplied by Sanborn in his article about the Allhallows Staining burial in 1656: Might this not also refer to the Rev. Stephen's son Stephen Jr., born about 1594 and ordained at Oxford on 19 September 1613? At present it is not known when or where the younger Stephen died.