Recommender choice for admission to a MSc program
If possible, it is always better if you can get a good letter of recommendation from someone who has actually supervised your research, because they can directly comment on your promise as a researcher. At the master's level, however, I don't know if it's quite so important as at the doctoral level, particularly because some fields may not require a bachelor's thesis (they may have a senior project, laboratory, or design course instead). 

In the present circumstances, this would be one of those times where you should check with the places you're applying and ask if you can submit a third letter of recommendation. Then you get the advantage of having two people who know you well personally, plus someone who can comment on your research.