My 2 year old would son scratches ALL the time until the point he would be bleeding and have scratch marks sll over. Try buying a nurishing lotion like Aloe or even a eczema cream. He might just have really dry skin. Even if you apply lotion after bath time or before bedtime your sons skin could still be very dry,even if it feels silky soft.
Does he show any skin irritation, red bumps, dry rough patches of skin. It could be eczema. If you are truly concerned about the sratching talk to your pediatrician.
It doesn't sound like pin worms. If he did have worms he would be VERY uncomfortable at night, their favorite time to come out. That is when their host is the most calm and still so they come out. Also, if he did have worms there's a pretty good chance you'd see one around his anus or in his diaper.
Good luck.