It happened in the parking lot of the North Shore Sephardic Synagogue on Cuttermill Road around 6:30 p.m. Saturday.
The 28 folding chairs were found in the shape of a large 12' x 12' swastika.
The rabbi called police when he discovered the symbol.
Police arrested 16-year-old Erik Bracamonte on Saturday and 16-year-old Joseph Cianciulli early Sunday morning.
Both teens were charged with Aggravated Harassment in the 1st Degree.
They were released on an appearance ticket and will be back in the First District Court in Hempstead on December 3rd.