It looks like the 7.4V LiPo with step-down converter will be more efficient all-around. The currents are lower at the higher voltages, so less conduction losses in the converter, and the reduces extra current demanded from the battery.
Assuming for the same form-factor, a 7.4V LiPo is 2x3.7V LiPo's in series, where the 3.7V LiPo package would be 2x3.7V LiPo's in parallel.
R@7.4V = 2*Rbatt
R@3.7V = Rbatt/2
I@3.7V = 400mA5/3.7 = 540.5mA
I@7.4 = 400mA5/7.4 = 270.3 mA
Pwasted@3.7V = 540.5mA2 Rbatt/2 = 146.1Rbatt mW
Pwasted@7.6V = 270.3mA2 Rbatt2 = 146.1*Rbatt mW
If you had a step-up converter with the same efficiency as a step-down converter, then the answer would be "go with whatever is cheapest".
In this case it looks like the step-down from 7.4V to 5V is more efficient which helps you at both ends. Because it wastes less power going from 7.4V to 5V, it uses less input current, which has lower loss in the battery itself.
In the step-up case, the conversion is less efficient, so it requires more current from the battery, so there is not only more loss in the conversion, but there is also more loss in the battery.