In which section of a research paper is it best to justify the choice of methods? I'm currently writing the methodology section of my thesis and wondered if  I was including too much.

In the methodology section I have currently included:


Alternative approaches I considered 
The pros/cons of those approaches/applicability to this project
Why I selected the approach I used


This information is needed somewhere but it is resulting in a very long methodology which is going a lot deeper into "Why I chose this approach" than "Here's how I did the research".

Does this "Why" discussion belong in the methodology section of a research paper or should it be placed somewhere else? If so, where?

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As an example: I can either survey people or perform an analysis of existing discussions on the topic. There are pros/cons to each approach (sample size, recruitment, etc) . The approach I choose will impact the research but I want to discuss the differences in the possible approaches and explain my reasoning for my choice.
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.