I responded to a similar thread just a few weeks ago. I live North of Boston and have a great pediatrician, Dr. Horowitz in Danvers. He's an MD and a homeopath, unfortunately he also has a waiting list for his practice.
In Jamaica Plain there is a Christine Luthra, MD and homeopath.
In Brookline there is Janet Levatin, MD and homeopath, she won't vaccinate so some insurance companies won't cover her as a pediatrician.
At Wellesley Pediatric Associates in Weston or Medfield. There Mark Blumenthal who although not an AP doctor per se, he is not one to "poo-poo" AP parenting practices.
Dr. Ann Becker of Newton-Wellesley Family Pediatrics, personally practices/d family bed and is very supportive of AP practices.
The only one I know personally is Dr. Horowitz the rest were mentioned to me.
Hope this info helps.