It depends on what you are using. If fingers or toys, lying down on your back, sitting in a chair, squatting, or kneeling.
I think if you wanted to milk the prostate you'd probably have to be squatting or kneeling to get the most fluid out.
I remember someone suggested the best position is to squat down and reach between your legs. Since the prostate is inside the anus and towards the front, hooking a finger towards your penis might be the easiest. The "squatting" can be varied, with your knees on the ground and your butt in the air (like doggie style), or laying on your back with your knees up. You can also try with a toy laying on your side with one leg up. In general, it helps to be very aroused and/or have an erection, especially close to climax because the prostate becomes engorged as well and you will be able to feel the prostate with your finger easier and feel the finger from the prostate itself.