Your son is appropriate height and weight, 75th for height and 90th for weight, usually those children that appear to have small penis size due to a fat pad are obese, really obese.
So penis size is a concern due to its relation to the pituitary, we become concerned about hypopituitarism, the hormones that the pituitary make include LH(which triggers some of the genitalia development), TSH( that dictates the thyroid), ACTH(that runs the adrenal gland) and growth hormone, so far your description does not sound like we have a low growth hormone level and good weight and height are another sign to me that they thyroid and adrenals are working fine as well. I would start with your pediatrician, they need to assess the "stretched length" and see how he compares to age standards, there is always variation, if he is in any doubt he can consult with a pediatric endocrinologist or even a urologist, some children may need a little testosterone if anything but more likely he will just need to be assessed. Other things may include a chordee-which is skin attached to the base that makes it appear shorter but is pulling on the skin. This is addressed by a urologist as well.
So start with your pediatrician