Hello Nishant Agrawal ,
I also encountered a similar problem during building libnfc-nci, please install "pkg-config" to overcome the current issue with command "sudo apt-get install pkg-config".
I installed the following packages before building libnfc-nci successfully.
$ sudo apt update
$ sudo apt-get install git make gcc g++ python autoconf automake libtool dh-autoreconf pkg-config
Thanks,
Yiping