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/usr/bin/pythontex3 is in texlive-extra-utils 2016.20170123-5.

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#!/bin/sh

if which python3 >/dev/null 2>&1
then
  python3 /usr/share/texlive/texmf-dist/scripts/pythontex/pythontex3.py \
    --interpreter python:python3 "$@"
else
  echo "You need to have python3 installed to be able to use" >&2
  echo "the Python 3 version of pythontex!" >&2
  echo "Exiting." >&2
fi