If you approach e.g. Jupiter you gain speed (it's pulling you in), which you then lose as you get away from it (as it's still pulling you in, meh). Gravity assists work because you use your chemical rocket right when you are closest and speed away, "robbing" Jupiter of the chance to claim the energy it lent you on approach.

Ion thrusters have very low thrust, so you would accelerate veeeeery slowly away from Jupiter's gravity well - and in this time it will keep affecting you and slowing you down, and the whole thing would be barely worth doing.

You could bolt on a very simple solid rocket booster just for the gravity assist, of course, but its ISP will be lower and you'll have to carry its mass until you can expend it.