Either would be a fine measure. They should be within .005" of each other anyway.
Technically, the bore size is the cylinder size but through wear you could actually be larger than one particular bore size and be relatively confusing. If you do measure the piston make sure you measure the intake to exhaust skirt distance 1/2"-3/4" up from the very bottom of the piston. The top of the piston is a few thousands smaller than the actual bore size to allow it to expand as it heats up. If you measure too far up the piston your numbers will be wrong.