Loud knocking noise coming from shifter area

A few weeks ago I noticed a knocking noise coming from the shifter area (automatic v6)while in reverse, I figured maybe a rock was stuck up by the flywheel since there is no dust cover on my trans. After inspection I didn't see anything lodged up there. The problem has progressed to while the car is in drive. I thought then maybe bad u-joints, and now I realize that it also makes that sound while in park from time to time so it cant be the u-joints as they're not in motion while in park. I have no clue. Any help is greatly appreciated! Thanks!