Disk brakes hands down. V-brakes are difficult to adjust, can get misaligned and destroy tire and rim (happens to me, very quickly). Disk brakes allows you to change your wheels easily and works even when wet and muddy. With v-brakes you always have the problem of different pad-to-rim separation for left and right pads due to differences in springs tension. Disk brakes works even if your wheel is wobbly.
For me, disk brakes (and overall weight) were the main reason for switching from supermarket steel MTB to a real aluminum MTB costing 4x more.