There are almost no "native" species left in any of the lakes (excluding superior).
If you want sustainable native great lakes ecology you need to cut them off from the oceans, re-reverse the flow of the Chicago and do a one-off massive trout and other native fish stocking. None of that is ever going to happen so until then we can keep experimenting with ecology and in that case Zebra muscles is much better than massive population booms and busts of alewives or other invasive fish species (Salmon were originally introduced to help keep the alewife population down)