Use the setup.cfg file in each project. This file is read by various Python-related tools, including pep8 (see pep8’s documentation) and flake8.
The documentation for setup.cfg with flake8 is in the Configuring Flake8 chapter. In short, you want a setup.cfg file with this content (obviously, adjust the 99 to your needs):
[flake8]
max-line-length = 99
If you don’t want to create a setup.cfg file, you can also specify this as an argument to the command:
flake8 --max-line-length 99