While the water quality of the lakes has slowly improved over the years, much of which is attributed to the invasion of zebra mussels and their incredible filtering effect, the nasty chemical levels still remain very high. Unfortunately, salmon, which is an oily species, stores many of these chemicals in the fatty tissue of the meat and just beneath the skin, primarily along the lateral line. Consequently, there are many species where the consumption quota is listed at zero, such as brown catfish, blue catfish, carp, sucker, and others.
The safest fish to consume are those that are fast growing and short lived. They don't have sufficient time to accumulate high concentrations of chemicals in the fatty tissue. The same rules apply to many saltwater species as well. Chilean sea bass, Atlantic and Pacific wild caught salmon, American eel, Atlantic croaker, bluefish, king mackerel, wahoo, marlin, swordfish and others are on the list of very small to no safe consumption levels. Most contain relatively high levels of mercury and PCBs - known carcinogens.
Most panfish species, porgy, Atlantic sea bass, grunt, tautog, etc..., are fairly fast growing and safe to consume.
One of the secrets to insuring that you consume the lowest levels of nasties is to skin and fillet your catch as quickly as possible, then remove all the dark meat along the lateral line. This should be followed by thoroughly rinsing your fillets with cold, fresh water and blotting the fillets dry before cooking. I you intend to freeze the fillets, the best technique is to place the fillets in a vacuum sealing bag along with a small quantity of water, then vacuum seal them. Frozen fillets using this technique can last up to six months without loosing the fresh taste.
Hope this helps,