Hello Pratyush Tomar,
As far as I know there is not a layer you can add in Yocto directly but you may use the current libnfc-nci repository (link below) as source and write your own layer and recipe to integrate libnfc-nci to your application or BSP.
GitHub - NXPNFCLinux/nxp-pn5xx: NXP's NFC Open Source Kernel mode driver
There is some information on how to integrate the libraries to Linux in AN11697 (link below)
http://www.nxp.com/documents/application_note/AN11697.pdf
As for the difference between the two, libnfi is an open source library that allows you to communicate with NFC devices while the libnfc-nci is the native library providing NFC functionality for which extension is added to support NXP proprietary features (e.g. MIFARE classic support).
I hope this information helps!
Regards,
