Total of three as both options utilize your Bonus Action for that turn.
PHB P78
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.
Since you only get one Bonus Action in your turn you choose one or the other.