This is an excellent question that needs to be discussed personally with a doctor
who knows you and your situation well. Your primary care doctor
or OB/GYN (whoever does your routine annual preventive checkups such as a pap smear, as well as whoever follows up your control of your autoimmune condition) would be able to advise you about who would be the ideal obstetrician to advise you further in this matter. Additionally, your doctor who is helping you manage your condition would be able to advise you about the feasibility of carrying a baby. Given the advances in medicine, it is quite possible that you will be able to have a baby, but it would be likely that you would need close follow up with multiple physicians involving multiple areas of expertise. An OB/GYN doctor who specializes in high risk pregnancies would be familiar with your sort of unique question, and would be most adept at coordinating the care that will be needed for you and your (potential) baby. Additionally, he or she could refer you to a geneticist
to discuss whether or not your child would be at risk for having a similar autoimmune condition as well.