The US Navy has been quietly mapping ocean bottoms for decades, since nuclear submarines started going all over the oceans.[1] The resolution isn't all that great, but by now they know where most of the seamounts are. It's a boring job. Cruise across ocean in a straight line towing a sonar array, return along a parallel track, repeat.

But maybe nobody has bothered to do the Great Lakes in detail yet. Not much submarine traffic.

[1] http://oceanexplorer.noaa.gov/explorations/lewis_clark01/bac...

A radioisotope might work, though good luck convincing people to dump tonnes of radioactive marker into a hole that nobody knows where it goes. A pinger from an aeroplane would do an alright job, but they are usually specified to work for a week which might be far longer than the period underwater.