Hi,
Based on my research, Microsoft NPS can support some third-party applications. NPS includes many enhancements to facilitate deployment of authenticated network access, to provide
extensibility for third-party components, and to support the latest networking technologies and platforms.
Third-party software vendors or Microsoft can provide additional NAP Enforcement Servers (ESs) for the NAP platform. A NAP ES obtains the System Statement of Health (SSoH) from
its corresponding NAP Enforcement Client (EC) and sends it to an NAP health policy server as a RADIUS vendor-specific attribute of RADIUS Access-Request message.
We have some ways could allow Third-party software vendors to extend NAP platform. More information, please refer to the bellows:
NAP Server-side Architecture
http://msdn.microsoft.com/en-us/library/windows/desktop/cc895519(v=vs.85).aspx
In addition, here are all the list of partners for NAP:
http://blogs.technet.com/b/nap/archive/2008/09/30/system-health-agents-shas-and-system-health-validators-shvs-that-are-available-from-nap-partners.aspx
I hope this helps!