Sony A99 II has a 42.0MP Full frame (35.9 x 24 mm ) sized BSI-CMOS sensor and features Bionz X processor. On the other hand, Canon 6D MII has a 26.0MP Full frame (35.9 x 24 mm ) sized CMOS sensor and features DIGIC 7 processor.
Sony A99 II's sensor provides 16MP more than Canon 6D MII'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 A99 II and 6D MII sensor size comparison.
Sony A99 II and Canon 6D MII 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 Canon 6D MII has 62% larger pixel area (33.19µm2 vs 20.43µm2) compared to Sony A99 II, it has larger pixel area to collect light hence potential to have less noise in low light / High ISO images.
DxOMark Sensor Scores
Both Sony A99 II and Canon 6D MII sensors have been tested by DxoMark. DxoMark scores camera sensors for color depth (DXO Portrait), dynamic range (DXO Landscape) and low-light sensitivity (DXO Sports), and also gives them an overall score. Of the two cameras that we are comparing, A99 II has scored 92, 7 points higher than 6D MII.