Elevation has nothing to do with when the sun rises or sets. Thunder Bay is on the extreme western edge of the Eastern Time Zone, hence the late sunset. You can witness the same phenomenon happen in Williston, North Dakota where the sun stays up until 9:58 on the longest day of the year, because it's on the extreme western edge of the Central Time Zone.
It's really all about how far east/west you are in a timezone that affects what time the sun rises and sets.
Just to add to your point to really exaggerate it: If you travel a little bit West from Williston, and now find yourself in the Mountain time zone, your sunset will be at 8:58 on the same day that it is 9:58 in Williston.
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