There is a 1.4 and 1.8 in the AF-S series, and a 1.4 and 1.8 in the AF-D series, and then there is the AI-S series, which has, at least, a 1.4 still in production. So, "which is best" can be a complex question, and can depend upon the conditions. I own the AF 1.8D, and the AF-S 1.4, and find each to be better for different things. The powerful focusing motor in my F6 will whip the 1.8D right quickly into focus, and the aperture ring allows me to use the 1.8D on a manual-focus FM3A, or with a Novoflex adapter, on my Canons. The 1.4 AF-S has a gasket at the base, which provides a weather-seal when used on my weather-resistant F6. The 1.4 lets more light into the camera, very useful at night. The lack of an aperture ring means I cannot use the 1.4 AF-S on a manual-focus camera, or with an adapter on my Canons, unless I am content with f/22.
At the time I bought my 1.8D, I was actually favoring the 1.8 AF-S, with the 1.4 AF-S a second choice, but none were in stock, anywhere. So, I bought the 1.8D. Then, a week later, a local dealer finally received two of the 1.4 AF-S lenses, and as weather-sealing was important at the time, I bought one of them, too, in spite of the focal length duplication. A part of me wanted to experiment with the AF-D and AF-S difference, anyway.
Sometimes, it makes no difference which I use, and the 1.8D gets the nod, simply due to its compactness.
So, neither of my two 50mm auto-focusing Nikkors is clearly better than the other. Then, there is my manual-focus 1.2 AI-S. I use all three of these, at different times, depending upon what I want to accomplish. Life is good!