I highly doubt you would be riding uphill all of the time, unless it's a bike at the gym.
Burning the most calories comes from a combination of increased heart rate and resistance. For example, if you use an elliptical machine with no resistance you will burn significantly less calories than if you up the resistance on the machine.
So, in my opinion running requires more effort and in my experiences elevates my heart rate more (especially if you run on an incline). Bike riding is MUCH easier on your knees, feet and hips though.