The installation of PyPDF4 is as simple as what is documented on its PyPI site:
pip3 install PyPDF4
When you install the Python 3.9.1 package from Python.org, it is installed in:
/Library/Frameworks/Python.framework/Versions/3.9
and the executables in that associated bin directory are linked into /usr/local/bin, including python3, idle3, and pip3.
That installer also updates a specific PATH environment in the ~/.bash_profile placing that Python3 library path at the beginning of your existing PATH environment variable. It does not automatically do this for ~/.zshrc, so caveat emptor should you be running zsh instead of bash.
The importance of this PATH adjustment is that when you run python3 or attempt to install any third-party packages into it, they go into this 3.9 distribution, and nowhere else, and the System Python 2.7.16, or the Python 3.8.2 distribution installed by the command-line tools for Xcode 11 and later — do not mess with you.
I actually created a Python 3.9.1 virtual environment (venv) in a folder, where I install all of my third-party packages (pyobjc, pyinstaller, PyQt5, etc.) and when I activate the venv and change directory into it, I am isolated from all other Pythons.