Edge Detection
What does it mean to "see" a molecule? I mean, every time you look into the sky, you are seeing all of the individual air molecules. I think you find that unsatisfactory because you can't distinguish between them. But you may see a tiny speck of dust floating through the air and say: "But I can see the dust particle!" What that means is that you can pick out the particle from the background of whatever scene your eyes are trained on. And in neural terms, it means that some sensors in your eye "see" the particle, and some sensors right next to them see "no particle", and your brain infers a boundary there that you interpret as "edge of particle".
So to see an individual object, you need to detect far more than a single photon. You need to detect many of them, because you need to trigger the edge detectors in your visual cortex, which receive input from numerous optical neurons.
Contrast
Secondly, there needs to be contrast between the "object" and the background. A speck of dust has high contrast because it is usually dark relative to the air it is floating through. Of course, you can't see it against a dark background, so you will only see very small dust under very bright lighting conditions. This is actually how edge detection works. The world isn't made of "lines". Our visual cortex infers the lines because some visual neurons detect light and its neighbors detect dark. If there is no contrast, there are no lines. If there are no lines, there are no edges. If there are no edges, there is no object to "see". An air molecule has no contrast relative to its neighbors. In the same way, a paint molecule on a uniformly painted wall has no contrast relative to its neighbors, which is why you can't pick them out either.
Limits
Now, suppose that we could make a single air molecule much darker or brighter than its neighbors. If it's darker, you will never know, because it will simply lower the average luminous intensity of that part of your visual field by an undetectably low amount. However, if it's bright enough, it may be detected as a point source. What will this look like? Will it "look like a molecule"? No, of course not. It will simply be a tiny fuzzy dot, bouncing around due to Brownian motion. The bouncing will make it appear much larger than it is due to persistence. But it will look similar to the faintest stars you can see, in terms of size.
The problem, however, is whether you will actually know that you are seeing this unusual anomaly. You see, vision, like every other process in the body, is noisy. Just look at a blank screen or wall. Does it look perfectly uniform? Most likely, you can notice color variations across your visual field, and tiny amounts of movement. Some people even see dots marching across their eyes when they close them or its very dark. Several factors are at play here. One is that neurons themselves are noisy, and do not fire with 100% accuracy (sometimes they will fire when they shouldn't, or fail to fire when they should). Another is persistence of vision: your visual cortex holds onto an image so it can compare movement and construct a smoothly moving visual field (which is why you can see ghosts when you switch from a bright image to a blank wall). Yet another is the fact that blood vessels run in front of your retina. Some people can see blood cells flowing across their retinas (mostly immune cells). All of these factors tend to wash out the detection of phenomena at the limits of our vision.
So, well before you reach the angular resolution limit of your eyeballs, or the cone density in your fovea, you will have to accept that many visual phenomena are simply limited by the amount of noise in the visual system, both the eyeball and the brain. The tiniest specks of dust you can see floating through the air are on the order of tens to hundreds of microns across. Air molecules are many orders of magnitude smaller than that.