Consider searching for a new job before you approach your boss with your plans to break-up. Ending a sexual relationship with your boss not only puts your job at risk, it also means a lot of awkwardness is soon to follow, for both of you. You can make it easier on yourself and your boss, if he becomes your ex-boss at the same time he becomes your ex-lover.
Choose the right time to speak to your boss about the break-up. Don't do it in the office, in fact, don't do it on a day that you must both work the next day. Speak to her on a Friday so that you both have the weekend to calm down and come to your senses. By Monday, hopefully, the initial emotions will have passed enough for you both to work together like civilized adults.
Be patient and choose a moment to discuss the break-up when you are both calm and stress free. Your boss has a difficult job, so laying the news on them the week before an important deadline or some other office crisis will not make the break-up go smoothly. If you must, wait until the next weekend. It won't kill you and waiting for a calm and tranquil moment may help save you from a lot of ugliness.
Prepare yourself before the discussion. Organize your thoughts the best you can, exploring all of the possible things you might say. Even if your boss gets upset, screams, yells, or cries it is extremely important that you maintain your calm and don't say anything you will later wish you hadn't. Your complete preparation will help you to keep your cool when the perfect moment comes along.
Be completely honest with your boss. Let him know all the things that attracted you to him in the first place, but that risking your professional career or his isn't worth it. Whatever your reason for the break-up, don't be ugly or critical. Be an adult and approach the situation calmly and with all honesty.