The OP provides an nicely detailed self answer, but I would like to add that when such areas exist, they are of particular concern to mariners1, and are therefore well-documented for nautical navigation purposes. I will use as my example an area at the north-eastern end of Lake Ontario, as it begins to meet the St. Lawrence River. The anomaly lies in the channel between the city of Kingston, ON on the mainland and Wolfe Island, in Canadian waters2.
NOAA chart 14802 covers this area. If you follow this link and zoom in, you will read this annotation on the chart:
AREA OF MAGNETIC DISTURBANCE
Further, the booklet for this chart series tells us on on page 2 that:
Local magnetic disturbances. –Differences from normal variation of
about 006°W to 007°E have been observed at numerous locations
throughout Lake Ontario. Differences of up to 37° have been observed in
the approach to Kingston, ON, on the north side of the head of the St.
Another good source, though not official, for Great Lakes boating information is creatively named great-lakes-sailing.com. Their page for Kingston tells us:
The Kingston water front area is affected by a strong magnetic anomaly caused by mineral deposits in the immediate area. The CHS pilot books for both the Great Lakes and the St. Lawrence River describe it thus:
"The normal variation of the compass for the shores adjacent to Kingston Harbour was about 12 degrees west, but along the front of the city it is not less than 18 degrees in the same direction. At the Government Drydock [Kingston Shipyards] it is as much as 30 degrees west, and abreast the Penitentiary it is 18 degrees east. A short distance west of Rockwood Asylum, the variation is again normal. Midway between Pt. Frederick and Garden Island, the amount of westerly variation is 20 degrees. At Simcoe Island it is again normal."
The morale of my story is, if using a compass for navigation in unknown waters, obtain the charts and Coast Pilot for the area and review them in advance.
1 I assume the same is true for aviators, but I am a boater, not a pilot, so I write what I know.
2 I feel a little guilty about providing U.S. Government sources for a Canadian thing. Apologies to Canadian Readers.