There are two parts in this. In NPS, the connection to the domain from the NPS server is Kerberos authenticated, as is the same situation with ClearPass.
There is no way to run the actual MS-CHAPv2 authentication with Kerberos, as NTLM is the only defined authentication scheme in MS-CHAPv2.
Moving to NPS will not change that in any way as it cannot change the standards. As Tim said, if NTLM cannot be used by policy, you cannot deploy PEAP/MSCHAPv2, and should move to other authentication methods.