MonkeyType is Python 3-centric, PyAnnotate is Python 2-centric.

PyAnnotate couples re-applying the types with the tool, and uses type comments for this.

MonkeyType generates .pyi files that you can either use directly or re-apply them to your code as proper type annotations.

Other than that, MonkeyType is used on a daily basis internally and solves a bunch of common annoyances of systems like these, like duplicates in unions, applying better types to stuff that was already hand-annotated with Any, etc.