Regardless of the context, the "best" measure/scoring (or in this case NPV fomulation) is ambiguous. If the aim is minimising cost in long-term, then obviously the present value of the long-term cash flows. If the aim is maximising energy output, then obviously it would be different.
I'm a big fan of the IRR approach for ranking projects. But none of these cash flow methods takes into account the opportunity costs of negative externalities.