In which section of a research paper is it best to justify the choice of methods?
Methodology section should focus on your own method (or algorithms or mathematical modeling) for the research.


Alternative approaches should also be discussed there in the same section precisely (if the alternatives are not highly different from the principal trunk).
The pros/cons of your approaches should be discussed in "Results and Discussion" or in the "Conclusion" section with points.
Why you selected the approach belongs to "Introduction" along with a small statement in "Methodology" itself.


Overall, methodology section tells the story of "HOW" rather than too much of "WHY". "WHY" should belong to introduction.