My 3 year old son has small pimple like bumps that don't bother him on his stomach, that wont go away; should I take him to his doctor?

Rash. All rashes are best assessed in person with your doctor. Rashes are usually a visual diagnosis. Your child's rash could be anything from a viral wart called molluscum contagiosum to scarlett fever to a viral rash. Thus is why you need to see your doctor.
Yes. From your description, there are a few possible causes, including skin cysts, molluscum contagiosum, and folliculitis. Some causes require treatment and some don't;your son's doctor can tell you the diagnosis and what treatment is needed, if any.