Squeal/Warble sound coming from aftermarket sound system

Hey guys, so I will try to explain my problem as easily as possible. So I have a 1999 Lexus ES 300. About six months ago I had a Boss amp and two 12'' Rockford Fosgate subs installed. I also installed Kicker speakers in all four doors. Everything was fine with stock Lexus sound system. Couple weeks ago I decided to get an aftermarket deck, a Pioneer. I had it installed 3 days ago. Noticed that when music was not cranked up, there was a warbling squeal coming from my system. Took it back. They reccomended a ground loop isolator. Just had it installed. No change to squealing. When they were messing around with jacks on back of deck, when they disconnected my antenna, it sounded fine. So...from what I have gathered from this thread it sounds like it is a problem with the ground wiring. The people who installed it suggested I have wiring bypass the stock amp in my Lexus, and that would fix it. What would you guys do? Rewire ground wires for stock amp? I really dont wanna lose radio even though now I am mostly using BlueTooth. This whole thing is very frustrating. Basically can someone tell me what they believe is wrong, and or what I should do to solve the issue. Thank you
Adam

Okay so update. After having done quite a bit of additional research and calling CrutchField for input, they have come to the conclusion that it is either me needing a antenna noise filter which might help, or they suggest I have all the ground wires inspected and or replaced or make sure they have a solid connection to something like chasis of my car. I like to figure things out logically and with deductive reasoning. So, if the system sounded perfect when they disconnected the antenna I am being led to believe that it must be something related to that and or my main power source/wiring. Should I try getting the 12$ antenna noise filter, or have them inspect my ground wiring?