First let me caveat the comments below with the statement that I am not a scholar of Japanese linguistics. I have some knowledge of the culture and of entymology that allow me to make the supposition below.
I have to disagree (with you and Merriam-Webster). The Japanese word tsu means steal. Nami does in fact mean wave and is one of four words that means wave. But tsunami does not mean harbor wave anymore than kamikaze means Divine Wind (the colloquial English translation). The word harbor is an English word introduced to Japan for which the Japanese equivalent is ha-ba (sort of like basuboru means baseball in Japanese). As near as I can find there is no actual Japanese word for harbor.
In researching (granted in a limited way as I don’t have tons of Japanese resources at my fingertips) the word breakdown the word tsunami can be broken into the two words tsuna and mi. Tsuna means either tuna (probably a modernization, see basuboru) or rope, while one meaning of mi is sword and it is the most appropriate in context. A rope can be fluid when in motion, and a sword causes great destruction, hence this is, in my opinion and based on what I know of Japanese culture and general etymology, the more likely candidate for a sword that moves like a rope.