The guys on the ship were ready with every kind of weapon that they could get their hands on. In the videos I saw, they were clubbing the Israel's with long metal bars. And then throwing one over down to a lower deck. And I saw several knives (though they were mysteriously cropped out of Reuters photos).
Report: Two police wounded by grenade outside Ukraine parliament (Reuters)
from the article: Blair hails deal with Netanyahu to ease Gaza blockade