I lived in Whitehorse for a few years and were able to hook into a number of Inconnu (Shee fish) in the time we lived there.
We found most of the Inconnu right on the mudline - the part where the river would dump into a lake where the mud and fresh water meet. We found that most of our catches were a by-catch while fishing for lakers. In the mud line, we found that downriggers, down to flashers, and teasers were the ticket. However, we also found that in Lake Laberge, one or two feet off bottom up on top of a shelf (this time of year up north - target 40 to 50 feet is as deep as you need to go) - again on the flashers/teaser combo.
As these fish can be big and aggressive (up to 25lbs or so), match the available forage and and you should have luck. Herring up to 8" inches seemed to attract them best IMO.
Good luck!
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