Try rotdoctor.com It is a wood saturation epoxy that penetrates deep and there is a filler to put on after that dries to fill in the rotted areas. look at the descriptions to figure out which product suits your needs. A bit pricey but cheaper than the alternatives. This is assuming the sill is not completely gone and is repairable. Easier than tearing out the sill and replacing. If they are very old windows you may wish to replace for energy efficiency
"Lazy people think of the easy way to do the hard stuff"