It was Legal

Interception of the Gaza Flotilla - Legal Aspects
According to the Laws of Armed Conflict, a state party to an armed conflict has the right to establish a naval blockade on its enemy's coast for security reasons. The power to impose a naval blockade is well established under customary international law.
Passage of a vessel through a blockaded area or entrance into it without special entry or exit authorization from the State imposing the blockade is considered a breach of the blockade. Moreover, the State imposing the blockade may capture a vessel even prior to its entering the blockaded area. Capture of a vessel attempting to breach a naval blockade can be done in international waters, before entrance to the blockaded area. (IDF Military Advocate General)