I've been working under the assumption for some time that produce that you were going to peel was mostly safe to buy conventionally (in terms of eating, not human rights, or carbon footprint). We were in a pinch a while back and bought some conventional apples that we peeled, but there was still a distinctive chemical taste even in the center of the apple.
It depends on the pesticide. Some are systemic and are picked up and distributed through the entire plant, although some tissues may have higher concentrations than others.
It's not all ground water related either. Some pesticides (such as imidacloprid) are used intentionally for their systemic affects. Some such as Dieldrin (off the market) are highly persistant and picked up from soil for years after application.
Good places for more info:
I think thicker-skinned fruits are probably the ones that are safest if you peel them (oranges, bananas, etc.). Not sure how protective the thin apple skin is as far as the chemicals getting through.