Citing in Footnote or Bibliography
This should be guided by 1. your institution's requirements for your thesis; 2. the standards of the citation guide referenced by your institution.

For example, most colleges have an Office of Graduate Studies to whom the final thesis must be submitted for final approval and archiving. They will have a "style guide" that includes rules about citations. These rules could indicate, for instance, the Chicago Manual style, APA, or Harvard citation style, which in turn will tell you how to handle the on-line articles.