I was always getting some false positives with PyInstaller from VirusTotal. This is how I fixed it:
PyInstaller comes with pre-compiled bootloader binaries for different OSs. I suggest compile them by yourself on your machine. Make sure everything is consistent on your machine. For Windows 64-bit, install Python 64-bit. Download PyInstaller 64-bit for Windows. Make sure Visual Studio (VS) corresponding to your Python is installed, check below:
https://wiki.python.org/moin/WindowsCompilers
Compile the bootloader of PyInstaller on your machine with VS. It automatically updates the run.exe, runw.exe, run_d.exe, runw_d.exe in DownloadedPyinstallerFolder\PyInstaller\bootloader\Windows-64bit. Check below for more info on how to compile the bootloader:
https://pyinstaller.readthedocs.io/en/stable/bootloader-building.html
At the end, install PyInstaller. Within the PyInstaller directory, run
python setup.py install