This could just be smaller than normal but good vision, Right now it is hard to tell because they are not focusing well. You may want to get an eye doctor to see if your regular doctor thinks the yes are small

We would have to see the baby and review both and family history to be certain, because many factors play a role in eye size and possibilities of visual changes.

Your statement of your son having "small eyes" can be very relative. To see if it is of concern, one must examine him personally. His pediatrician should be the first evaluator.

Does he have trouble seeing now?

If they are truly small eyes, I would take him to a pediatric ophthalmologist for at least one visit to make sure that everything else with his eyes is ok. This will give you and your doctor reassurance for the future.

There is a wide range of what is normal. It's hard to answer your question without seeing your son. It will probably not affect his eyesight. If concerned, you should take him to an eye doctor