Sony A6000 has a 24.0MP APS-C (23.5 x 15.6 mm ) sized CMOS sensor and features Bionz X processor. On the other hand, Samsung NX1 has a 28.0MP APS-C (23.5 x 15.7 mm ) sized BSI-CMOS sensor and features DRIMe 5 processor.
Another difference between these two cameras is that Samsung NX1's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moire occurring in certain scenes.
Below you can see the A6000 and NX1 sensor size comparison.
Sony A6000 and Samsung NX1 have almost the same sensor size so none of them has any significant advantage over other in this area.