Many variants of this exist, but the earliest known incident of such a comment appears to be a partial quote from James Waterman Wise, Jr., reported in a 1936 issue of The Christian Century: "in a recent address here before the liberal John Reed club [Wise] said that Hearst and Coughlin are the two chief exponents of fascism in America. If fascism comes, he added, it will not be identified with any 'shirt' movement, nor with an 'insignia,' but it will probably be 'wrapped up in the American flag and heralded as a plea for liberty and preservation of the constitution.'"
Another early quote is that of Halford E. Luccock, in Keeping Life Out of Confusion (1938): "When and if fascism comes to America it will not be labeled 'made in Germany'; it will not be marked with a swastika; it will not even be called fascism; it will be called, of course, 'Americanism.'" (This quote is also attributed in a New York Times article from September 12, 1938, page 15 as having been given in one of Luccock's sermons.)
Harrison Evans Salisbury in 1971 remarked about Lewis: "Sinclair Lewis aptly predicted in It Can't Happen Here that if fascism came to America it would come wrapped in the flag and whistling 'The Star Spangled Banner.'"
Source: The Christian Century, Volume 53, Feb 5, 1936, p. 245
Source: Misattributed, p. 29, The Many Americas Shall Be One, Harrison Evans Salisbury. Published by W. W. Norton, 1971.