I've used POR-15, both black & clear. The key to keeping paint on it is to get the M/C real clean, I've had good luck using Acetone. Hope this helps.
I see Eastwood sells a product for painting master cylinders...I've never tried it though. 2K Spray Gray Epoxy Paint w/Stainless Additive http://www.eastwoodco.com/jump.jsp?itemID=23997&itemType=PRODUCT
I have used "cast blast" in aluminum or cast iron colors its available at your local parts store, made by the same people that make engine enamel.The trick is to clean the mc well and try not to spill brake fluid on it.