Aquathol K at 3 ppm is effective at controlling naiad. This would be 1.9 gallons per acre foot. For example, 1 acre, 5 feet deep would need about 10 gallons. I would suspect in your area the cooler (cold) weather would result in most of the biomass falling out. Next year I would wait until you feel you can't wait any longer and then do a treatment to control the bulk of the area where the naiad is. You should get some residual control outside of the "target" area by treating this way.
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