We just had a house inspected, and the inspector pointed out that black window mold is hard to avoid. Having a humidifier too high makes it worse, but condensation will happen anyway. It is not a bad window, nor are you doing anything wrong.
I researched the toxicity of such mold, since I figured if I have to live with it, might as well find out how bad it is. It's not terrible! Whew! While drywall mold can be toxic...
I just cleaned my windows with bleach. It helped but I could not get all the nooks. I have severe breathing problems, plus a baby...but it's not from a little black window mold. We just rented here and it came with the house. So, clean the best you can.