Clinton, but Trump might win Suffolk.
Clinton will win both counties.
Suffolk is more downballot Democratic than Nassau; it has a Democratic County Executive and a Democrat-controlled County Legislature. Nassau has a FAR stronger GOP, and always has, but it also has more liberal Jewish voters (some of them registered Republicans) and has always been more Democratic than Suffolk in Presidential elections. Suffolk's Democratic organization is far stronger than Nassau's, however.
If Trump carries either of these counties, he will have run a far better campaign than he's running now.