I like measuring with fat calipers best. With them you pinch a certain spot on your side near the hipbone. When the calipers click they leave a measurement for you to read, you compare those numbers with a chart and that tells you your fat percentage. It has to do with your age as well so the chart takes those factors into consideration.
I've taken these measurements and compared them with the online methods and mostly they were similar in numbers. My body fat scale though does not give an accurate reading as far as I can tell, it will change by many points depending on whether one is well hydrated or not. With Atkins (when I'm seriously on it) my hydration levels go down, so my fat percentages go up (or something like that) on the scale. That of course isn't what I want to see when I know that it is just because of a change in water levels. So I don't trust the scale much.
With the calipers I can measure in a way that is most accurate for me.