Yes, Israel obeyed international law when it raided the Gaza flotilla, because it was only reacting to what was aggression from another nation. International law allows Israel to defend itself when it is attacked. Israel was attacked and properly raided the Gaza flotilla in response. International law allows Israel to defend itself.
The raid occurred in international waters and the flotilla had the right to be there. Reports also indicated that Israel used excessive force to subdue the flotilla, and because of these facts, it would appear that Israel did not obey international law. The flotilla ships also did not carry weapons, so they didn't pose a threat to Israel at the time of the raid.