This is a very good question, and I have yet to see a miracle answer that I have wanted to hear lol.
SOme back muscle and a rake has done some good for my pond. This is only good for the edges of the pond though. I, like many others, need a solution for weeds out in the middle of my pond. The rake on a rope ordeal didn't pan out for me. The rake takes forever to sink, doesn't sink right, can't get weights on it to do any good and dig in anyway... lol. (Home-made jobby of course, I am sure a pond rake built for this works 100x better)
I have yet to do this, but something I have been looking for is some old bed springs. I have heard these work pretty good if you have a tractor or winch or something to pull them across the pond bottom. This may turn out to be more work than its worth, but it is something I am going to try eventually.
Good luck!