There are issues with vaccination safety and what substance they use to preserve the vaccinations. I don't know if I buy the links proposed between mercury and autism, but some practices will provide mercury-free vaccinations, so that is what I've always looked for.
Also, it is somewhat helpful if the ped is on the same page with you in terms of basic parenting philosophy, especially when the baby is young. I know you're going to nurse, so a ped that is pro-nursing would be good. If you have nursing problems and the ped is not pro-nursing, they will be quick to push formula before other solutions have been explored.
You might want to go to a La Leche meeting or talk to a lactation consultant to see what pediatrician they would recommend. Just be aware their pick may be completely on the earthy-crunchy end of the spectrum, with a bias toward attachment parenting, family bed, etc.
(Just as an aside, our first pediatrician was a practicing member of Opus Dei
and he worked out just fine. I conveniently failed to mention this detail to my liberal Jewish parents.)
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