Since I was looking for this as well and just figured it out I thought I would share.
Use adsutil.vbs (located in C:\Inetpub\AdminScripts)
from the commandline:
adsutil.vbs CREATE w3svc/AppPools/<app pool name> IIsApplicationPool
for example:
adsutil.vbs CREATE w3svc/AppPools/MyApplicationPool IIsApplicationPool
I hope this shortens someone else's search.
Best,
- Rich