You can certainly use the present perfect continuous without an expression of time. In such a case you are interested only in the activity, not in its starting point or duration. For example:
- Your shoes are wet. Have you been watering the plants?
If you want to emphasise when you started the activity, you need to use since:
- I've been watering the plants since 5 o'clock.
And if you want to emphasise the duration, you need to use for:
- I've been watering the plants for 5 minutes.
The specific question Have you been watering the plants for 5 minutes? is grammatical but unlikely. One possible scenario is that your wife has asked you to water the plants for 3 minutes only and suspects you might have exceeded the time limit she set.