There's no one-size-fits-all answer to that question. Every site is different, and what works for one might not work for another.
My personal experience is that ads at the foot of the page get the highest click-through rate. But that might be because of factors that are specific to my sites. It won't necessarily be the same for you.
As for it not annoying your users, that is highly subjective. My own rule is to place ads where they would not annoy me, on the assumption that my users will think the same way that I do (which isn't necessarily true).
The best thing you can do is to test it for yourself. Try above-the-fold on some pages, below-the-fold on others, and compare the results. That's the only way to know for sure.