Hmmm ... In Vagrant 1.2.2 and Puppet 3.2.3, I can set hiera_config to puppet.conf without any problems. I would double check that you are editing /etc/puppet.conf on Vagrant vm and not on the main machine, and that the hiera_config line is the [main] block, not just the [master] block.
If both of these conditions are true and still not working, you can try explicitly setting hiera_config in your Vagrantfile:
config.vm.provision :puppet do |puppet| ... puppet.options = '--hiera_config=/etc/hiera.yaml' end
Good luck
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