Lets say the lilies did cause this, which may be true, may be not. Say you remove the lilies and clean them in some way that kills every bit of whatever this is, which probably isn't possible without killing the plant. I don't see how that would fix anything. The stuff is in the pond.
If you're really freaked out by this black stuff you should remove and throw out the all plants. The pond should be emptied, power washed, and filled with water and treated with chlorine just like a swimming pool (shock treatment). If it is algae or a fungus you have to kill just about every bit of it. I wouldn't, but I don't know your level of anxiety over this. Many people like to do things to their ponds to lower anxiety, to feel they're doing something.
OR, figure out what it is and then come up with a plan. This does require some work, reading and learning. I don't know your desire level for this type of thing, many people are strongly adverse to this and will only except very simple "answers".
OR, let the pond deal with whatever it is. Your pond is very good at this. Bacteria, other plants and fungus, will all be testing this stuff and will at some point in this stuff's life cycle, figure out a way to eat it. Ponds are a constant cycle of some things eating other things. Some grow in population for awhile, some decline.
