If you want to tie the flies with dull beads, then any of the many chemical solutions will work..gun blue, oven cleaner, acids, coatings of various types (I'd use clear head cement with some baking powder in it to flatten it). OR, you can buy black beads. The ones from Larva Lace are a 'matte' finish and I really like them myself.

For 'on the water' use, the sharpie is the simplest. But, I prefer brown or green rather than black. The bead will still shine, but the color dampens the flash a bit.