Remember that all calorie calculator's (even a heart rate monitor which measures calories expended) are just estimates based on a mathematical equation (algorthim). The only accurate means of measuring calories expended would be in the laboratory setting with you hooked up to equipment that measures your oxygen intake and carbon dioxide output.
When you begin exercising your muscles demand a greater amount of oxygen to supply the body with energy to perform the task at hand. As your need for oxygen increases, so will your heart rate (to allow for increase blood flow to the working muscles), therefore, your heart rate monitor determines your calories burn by monitoring your heart rate. It isn't heart rate alone that determines calories expended, but the amount of oxygen one consumes doing the activity. This is why wearing a HRM outside formal exercise is futile...the algorithm is assuming your increased heart rate is due to activity and not just sitting in a car on a hot summer day.
So to make a long story short, I would use your HRM reading and if over time you see your weight loss stalling you may want to take an average of the calorie calculator and your HRM reading.