If you clear it up now the clay around the banks will wash in and muddy it right back up. You could thickly plant some annual rye and fescue seed mix, put down straw over it, and then try to clear it after a couple of months after the grass establishes. Anything to filter the clay from getting into the water will help a lot at this point. Bales of hay at the water's edge is another idea, along with planting the grass. Even laying sod, if you want to spend that much.
See this helpful link for wanting to clear a new clay bottom pond.
http://forums.pondboss.com/ubbthreads.php?ubb=showflat&Number=460821#Post460821
