it all depends on where in the great lakes you are. some areas are off limits due to being shipwreck sanctuaries. here in ohio you would have to deal with the ohio department of natural resources, and dr. charles "eddy" herdendorf. he is the states underwater archaeologist and he has been great to me with what I am doing. my claim pre dated the 1987 abandoned shipwreck act and has produced some extraordinary finds.
if you are talking fairly modern wrecks 1950 or newer I don't think there would be too much of a problem, depending on what you are planning to do. older than that you would have to have a good plan with state approval.