Depends on what you are doing and what you want to measure. If you got a generic chromatogram, say a run that you will always use for an analysis of a protein hydrolysate or for a combichem sample, you definitely use the gradient run time as the measure. For comparing the quality of a separation for a specific sample, say an impurity profile run under different circumstances, you are probably better off to use something close to the retention time of the last peak (just beyond the last peak).
The standard way to estimate the peak capacity is to use the 4-sigma peak width, which can be conveniently obtained from the software.
You will get different peak capacities when you vary the gradient parameters, such as the gradient slope. Peak capacity is not a parameter of the column, but a parameter of the separation. You change the separation conditions, you affect the peak capacity.
Here is a reference: U. D. Neue, The Theory of Peak Capacity in Gradient Elution, J. Chromatogr. A 1079 (2005), 153-161