For two phones listed above, the answer is indeterminate. Even though option 1 captures less light per pixel and thus has higher per-pixel noise, you can apply more noise reduction before the picture becomes too fuzzy to tolerate, which means you may still end up with a less noisy picture overall. And given that we're talking about only a 3.4% difference (see Jules's answer), I think it's pretty likely that the higher-resolution camera will yield better pictures.
With that said, I'd be remiss if I didn't point out that choosing the best smartphone for low-light photography is like choosing the best Ford Fiesta for moving a concert grand piano.
Even APS-C isn't great in low light. And the best cell phones aren't even what I would call good. As others have mentioned, the amount of light hitting a sensor is proportional to the surface area divided by the square of the aperture. So assume (for example) a 33 mm^2 cell phone sensor at f/1.8, you get:
33 / (1.8 * 1.8) = 10.2
Now if we fill in an APS (full frame) sensor:
864 / (x^2) = 10.2
we get x = 9.2. So for a given megapixel count, assuming all else is roughly equal, the full-frame camera gets more than 4.5 stops more light per pixel.
To put it another way, if you compared such a cell phone to a DSLR with an f/1.8 lens (apples to apples here), if the DSLR were shooting at ISO 100, the cell phone would have to use a longer shutter speed even at ISO 1600 (typically, a cell phone's max ISO).
Alternatively, if you keep the same ISO level (and thus, in theory, comparable noise levels), a full-frame sensor would take shots ~23x as fast. If the shot takes 1/100th of a second on a DSLR, then, you'd expect it to take a quarter second on the cell phone.
And this would likely remain true even if camera manufacturers stopped improving their large sensors right now, because there just isn't that much room for improvement in terms of how much light a sensor gathers at this point. No matter how much image stabilization you do, no matter how many times you try to take the shot and pick the best one, that's only going to get you a couple of stops, realistically. The other 2.75-ish stops make the difference between a high keeper rate and an appallingly bad keeper rate.
Plus with 30-ish megapixels on a modern FF camera instead of 12 or 16, you can apply much heavier noise reduction before the picture becomes too soft. :-)