The letter, reading "You are the people of Satan, Hell is waiting for you," was received at one of the synagogues during the weekend and the other on Monday morning, the source said.
Monday's attack saw a scooter-riding gunman shoot dead three children and a 30-year-old religious studies teacher at the school in the southwestern city of Toulouse.
The gunman opened fire on a crowd as children arrived for class, then charged onto school grounds. A fifth victim, a 17-year-old boy, was left in a critical condition. The gunman escaped.
Rights groups and the government denounced the attack as anti-Semitic.