Another take on the command raid of Tyre, this one from the Jerusalem Post: Naval commando unit raids Tyre. This article goes into a bit more detail than the Ynet story.
Note: Israel doesn't have a "navy" as a seperate entity like we do here in the USA, or like most Eurpean countries. The Israeli navy is actually under the command of the Israeli army: All forces combined, naval, air and ground, are the Israeli Defense Forces, or IDF.
This is speculation on my part, but what makes the commandos "naval" is that they probably took off from helicopters on Israeli Saar 5 class corvettes, and are most likely trained to operate from ships, much like American Navy SEALS, or British SBS.