Its a fairly mainstream solution but we've been fairly happy with Harvard Vanguard's Cambridge office, specifically Dr. Kruger. He's good with kids and he's pretty mellow about most things. I don't know how he'd feel about vaccinations being delayed but he was certainly sympathetic to our concerns and allowed us to avoid doing too many at one time.

I also like the connection to Children's Hospital (they do great stitches, which most kids will need at some point) and the fact that their urgent care center on weekends is the Davis Square building.