NYC determined that there was no credible threat, which is why they kept their schools open. LA (in light of the San Bernadino shooting) decided to err on the side of caution and shut down their schools.
Interestingly enough, although the threatening e-mail came to NYC and LA after being routed through Germany, the FBI thinks that it was originally sent from somewhere in the USA, and they are still looking for the original ISP address.
Additionally, although there were Islamic statements in the e-mail, they were phrased wrong as well as the writers didn't capitalize the word "allah".