"Who is heading the NY family in the Winegardner books?"

According to the books, Pentangeli was replaced as caporegime by Richie "Two-Guns" Nobilio, another former member of Clemenza's crew. Had Pentangeli not been selected to replace Clemenza in 1958, Nobilio probably would have then. But he was chosen in 1959, and was still caporegime as of late 1964, the year the books end. No idea what happens to him afterward, but there's a lot of time separating 1964 and 1979-1980, so he could be gone by Part III.