Do you know the oxidation states of tungsten and molybdenum in your solutions? If you have tungstate (WO42-, W6+) and molybdate (MoO42-, Mo6+), then adding any soluble salt of a divalent transition metal such as manganese nitrate will give you a mixture of metal tungstates and molybdates. If your goal is just to quantify the amount of tungsten in your solution, you could then do some powder x-ray and Rietveld analysis. If you actually want to separate them, this obviously won't work, and I can't think of anything that will help you. Maybe some sort of high-pressure anion-exchange column?