I just bought a house four months ago and there was large amount of
rocks.. A LARGE pile I should say.

We took the rocks and put them into large plastic containers. Then by
boyfriend dug a very large hole taller than he is (6 feet). The top
soil had tons of rocks in it as well. We pulled out good dirt, dumped
the rocks in and poured the good dirt over it. The task took about 3
weeks of daily labor..however it's been 2 months and the grass is
gorgeaous.

I have befor and after pics if your interested.

Though labor intensive I say dig a hole bury what you don't want and
cover it back up.