There is no single best methodology for qualitative research. It depends on your research questions and sample. Most of the researchers use interview, focus group, case studies etc. Nowadays analyzing data from social media, such as facebook status and tweets have also gain much attention.
The best method is the one that can address your research aim the best. so for each study, the answer will differ. It is also depending to the researcher. Since, in qualitative studies skills and experience of the researchers are very important, and of course, in addition to attending courses and trainings, and studying, one would need to involve in the field and actually do the job until they can experience and learn.
The efficiency of all the quantitative methods rests with the way the data is viewed and interrupted. As such, any method could be built up to a level.
I would also add that it depends upon what you are looking for. If you are inquiring into an experience, phenomenology would be the way to go. If you are seeking to understand a phenomenon that is shared by many (thus, moving toward a seed for a theory about a particular topic, such as child free by choice, for example) you might want to use Grounded Theory. Then, you would want to look at the different types of methods to determine which would suit your inquiry best: individual interviews, focus groups, even artistic research...This takes some time but is worth the effort! Please feel free to contact me to discuss further. [email protected].