We go to Hamilton Pediatrics. They're pro-vax, but we only see Dr. Haberman - he's pretty old school, and has never said a word to me about our non-vaxing. The other docs have made comments, and I feel that the other docs are more mainstream, but Dr. Haberman has been pretty easy going, common sense, and is not quick to jump on the new "thing" (like meds for baby reflux), at least in my experience. We don't see him that often to be honest, since we treat minor illness at home and haven't had anything serious happen, and stopped with the regular well-visits after 1yr. Granted things may have changed with them with regards to new patients, but if you're willing to deal with a doc who is non-vax "tolerant", Dr. Haberman is decent.
I have heard of Dr. Suzuki in Plainsboro who is supposedly supportive, but I can't say for sure. Dr. Ginsburg outside of Princeton is no-vax and a big vax choice advocate, but she doesn't take insurance so you've got out of network costs to consider. I've heard of a family doc in Ewing, Dr. Jass (I think that's his name??) but haven't checked him out yet either.
If you hear of anyone else, please do post and share!!