It depends.

Assuming both sensors have the same linear dimensions:

If you are viewing the images from both sensors at the same display size, then the low light performance of both will be similar, assuming they use the same generation of technology. There are other advantages unrelated to low light S/N performance that make using a higher resolution sensor and then downsizing the result slightly better for reproducing fine detail when images (and video) are shot under better light.

If you are viewing the images from each sensor at 100% magnification (1 image pixel = 1 screen pixel), then the image from the higher resolution sensor is being enlarged more and will have poorer low light performance, all other things being equal (which they never are).

There are also some scenarios with very small, very bright specular highlights, such as is the case with astrophotography, where the better performance of the sensor with larger photosites can be due to the smaller photosites (a/k/a sensels or pixel wells) on the higher resolution sensor having a lower full well capacity than the larger photosites of the lower resolution sensor. If the scene contains bright specular points, a larger sensel with only one specular point illuminating all of its surface will allow a brighter exposure before full saturation than a smaller sensel with the same specular highlight illuminating it.