Is the baby admitted to your facility?
The codes changed in for 2009, so I'm answering based on 2009 dates of service.
First, NO, you can't bill the transport code. Look at the guidelines on page 33 of 2009 CPT Professional edition: "... Only the time the physician spends in direct face-to-face contact with the patient during the transport should be reported..." (emphasis added by FTB)
Next, look at codes 99464 or 99465 (they cannot be billed together) to see if one of them accurately describes the service provided.
If the baby was admitted to your facility you may also be able to code 99468 Initial inpatient neonatal critical care.
If the child was NOT admitted, but your physician attended to the baby until transport could arrive, you'll be looking at codes 99464 or 99465 only.
In either case if the child needed to be intubated or vascular lines were required as part of the neonate's resuscitation (not just as a requirement for admit to the NICU), you can code those procedures separately.
Don't forget the -25 modifier on your E/M if you have additional procedures.
F Tessa Bartels, CPC, CEMC