That's the misunderstanding here, the convoy wasn't going to enter Israeli territory, it was going to Gaza. And a naval blockade means you stop ships in international waters, otherwise you'd have to enter the territorial waters of the country being blockaded. Of course this situation is a bit different as Gaza is not a country. And Turkey is the one who set the whole thing up, if Israelis still think Turkey is their friend, they're being delusional.
Israel has the right to police the naval approaches to the port of Gaza following the Oslo accord. In addition Israel has a 20 km buffer zone along its coastline I believe instigated to stop rocket boat attacks. All this means that Israel does indeed have a defined naval border, which was not breached.
There may be legal precedent for a search, but a midnight commando raid. That's not how you go about challenging an incursion you believe is about to take place. This is what they should have done : challenged the vessels the minute they entered Israeli territory and explained that their convoy was subject to search. Then sent in police and customs agents. If these agents were attacked, Israel would have had the moral high ground.