For GMT, you can find the citations at https://www.generic-mapping-tools.org/cite, bearing in mind that some of the modules have their own citation as well (e.g.
greenspline, etc). Since GMT is great in having had a paper out for almost every version, just cite whatever version you use, which is usually the latest (that would refer back to the older versions anyway). The current citation for GMT6 (in APA7 format) is:
Wessel, P., Luis, J., Uieda, L., Scharroo, R., Wobbe, F., Smith, W. H. F., & Tian, D. (2019). The Generic Mapping Tools Version 6. Geochemistry, Geophysics, Geosystems , 20 (11), 5556–5564. https://doi.org/10.1029/2019GC008515
As for PyGMT, there are a couple of ‘old’ posters dating back to 2017/2018 at https://www.pygmt.org/dev/overview.html. There’s a new 2019 AGU one at https://www.leouieda.com/posters/agu2019.html which might be better. (Note to potential contributors: would be great to add this to the website).
On a side note, it might be time to get a proper PyGMT v0.1.0 release out, and make a citable Zenodo DOI link out of that, or even put in up on JOSS. The stars are certainly aligning themselves. Someone requested for a PyPI release at https://github.com/GenericMappingTools/pygmt/issues/414 and I’ve submitted a corrected manuscript out for open review yesterday with PyGMT made figures. I’d be keen to make this happen if the team is too