A Leica R9 is a completely different camera than a Nikon FM3A. It‘s like comparing a Nikon F6 with a Leica R6.2. I have both, the R6.2 and the FM3A - excellent cameras and it is more a matter of taste which to prefer. Regarding lenses: Leica lenses are excellent, no question. But you can easily use Zeiss lenses including Milvus, Apo-Sonnar and Voigtländer lenses with the Nikon, if highest quality is relevant.
There are many advocates for the F3 in this forum. Nice camera, but the fading LCD in the viewfinder in these cameras are a no-go for me. In a couple of years all F3s will have dead viewfinders, in contrast to the FM3A.