Total of three as both options utilize your Bonus Action for that turn.
PHB P78, emphasis mine:
Flurry of Blows. Immediately after you take the Attack action on your turn, you can spend 1 ki point to make two unarmed strikes as a bonus action.
Then under Martial Arts:
When you use the Attack action with an unarmed strike or a monk weapon on your turn, you can make one unarmed strike as a bonus action. For example, if you take the Attack action and attack with a quarterstaff, you can also make an unarmed strike as a bonus action, assuming you haven't already taken a bonus action this turn. (ibid., emphasis mine)
Since you only get one Bonus Action in your turn you choose one or the other.
