There are multiple ways. From pcap, you can use wireshark (but I don't use that), captcp, and tcptrace. Personally I'm using captcp and also tshark, e.g.,
tshark -r your_pcap_file -z conv,tcp -q
gives you TCP throughput.
You can also use captcp to get per second throughput, and plot a figure there, using gnuplot for example:
captcp throughput -s 1 -i -f 1.1 -o one_folder your_pcap_file
I have a question for you too, how do you change TCP variant in NS3? Can you share me the code of doing that?