The Gibraltar-flagged Hercules Star and the Panama-flagged New Andros were damaged. The attacks push Gulf shipping insurance costs even higher.
Strikes on air defences and missile production sites are a response to Iran's October 1 attack. The Iranian army said four soldiers were killed.
Hamas and Iran's Revolutionary Guards said the head of the political bureau was killed at his residence. Israel has not commented.
The wreckage was found after an hours-long search in fog and mountainous terrain in the country's northwest. First Vice President Mohammad Mokhber assumes the presidency.
Tehran called the attack a response to the strike on its consulate in Damascus. The US, Britain, France and Jordan helped Israel defend itself.