I throw a stone to/towards you.
(Ne does indeed imply the physical act of throwing towards someone, keeping with the idea that verbs of motion use ne as the place towards which the motion is directed.)

I throw a stone to you
(The dative case would be used in the sense of giving the stone to someone, although there's some overlap here with ne.)

I throw a stone at you.
(And wä would have an aggressive connotation.)