I wouldn't use a heart rate monitor for non-aerobic activity. The formulas they use to estimate are based on your average heart rate for the activity compared to your programmed maximum heart rate. In a lab, calorie burn is measured by oxygen use beause during aerobic exercise your heart beats faster to supply oxygen to your muscles. Polar and others are estimating your oxygen use based on your heart rate and using that to estimate calorie burn. The same assumptions don't hold as true for non-cardio. Even for aerobic exercise it is an estimate based on averages and may guess high or low for you. But it is probably one of the better estimates for aerobic activity.
Fitbit, Jawbone, etc are motion based. The wrist worn devices might be okay, but I don't think they would pick up much. I personally wouldn't worry about it because doing office work doesn't actually burn that much more than your resting rate. It burns more, but not that much more. Have you looked at MET (metabolic equivalency for a task) charts? They compare intensity of all sorts of activities (including sedentary and occupational activities so not just exercise). METS can be used to estimate calorie burn as they are adjusted factoring in your resting metabolism. Sitting still is 1 MET, sleeping less than 1 and office work or seated work using hands is something like 1.5 METs. Walking 4.5 mph is 6 METS, I think jumping rope is about 10 METS. tHe fitbit activity database is based on METS adjusted for your stats so you could log office work during your work hours if you want. If you log an activity it changes the fitbit calorie burn accordingly. I log some of my workouts using my heart rate monitor quite often.
The device that I think may be most accurate for you... I don't have one, but I think a bodymedia/bodybug or similar. Those have an arm band with four sensors: motion, perspiration, body temperature and something else (they don't use heart rate, I had read they didn't consider it accurate for non-exercise). I don't know how accurate they are, but it is likely they would be pretty accurate as when metabolism is sped up your body temperature will be higher than when your metabolism is slowed down. I considered one when I was looking at my fitbit, but went with a fitbit because I couldn't see myself wearing an armband every day. I think they are considered among the more accurate activity trackers in terms of calorie burn though.
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