Measuring power consumption of system with buck converters
The method you're proposing is correct. Efficiency is (power out) / (power in).
The efficiency for the buck regulator varies with load, and may be fairly low at light load. The regulator datasheet will have an efficiency vs. load characteristic. Check that and see if this correlates with what you're seeing. If it does, you have your answer. If not, you may have some other problem with your design.