I have successfully used oxalic acid followed by sodium carbonate. General Motors has a TSB that can be found on the web explaining the process. I did it on a 90s 30KW John Deere powered generator that I was having overheating problems with. I tried several auto parts store flushes on it, they helped but did not solve the overheating. I was sure the radiator had more deposits in it so I hunted down the chemicals, wood bleach and washing soda, and gave it a try. I drained lots of chunky green and the orange water form that cooling system. It hasn't overheated sense.
I wouldn't be afraid to try it on a boat. Be sure to read the TSB. The sodium carbonate is rough on aluminum so don't use too much or run it too long. I ran it 2hrs with the acid and 20min with base.
It just occurred to me that you are probably trying to clear the raw water side of the heat exchanger. This might still be worth a try but you will have modify the method.
The green fluid is oxilac acid flush.
The orange is the sodium carbonate flush.
The brown is the parts store flush that I tried twice before.
Note, the pictures are name incorrectly. Sorry about that.