Nikon D610 has a 24.0MP Full frame (35.9 x 24 mm ) sized CMOS sensor and features Expeed 3 processor. On the other hand, Sony A99 II has a 42.0MP Full frame (35.9 x 24 mm ) sized BSI-CMOS sensor and features Bionz X processor. Sony A99 II's sensor provides 18MP more than Nikon D610's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Another difference between these two cameras is that Sony A99 II'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 D610 and A99 II sensor size comparison.
Nikon D610 and Sony A99 II have sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Nikon D610 has 74% larger pixel area compared to Sony A99 II, it has potential to collect more light on pixel level hence have less noise in low light / High ISO images.