Why 2000 though? I know Gore did extremely well in NY but still...
Gun control may have resonated with voters in these NY/NJ counties. Most basically I would posit that Bill Clinton was just extremely popular in the Northeast so Al Gore was quite a good candidate there in 2000.
Any ideas on these KY counties that swung against Gore, back to Kerry, and then right back to the GOP? They are all close to Elliott county, which if you will notice is by itself in voting for Gore but surrounded by like minded counties in voting for Kerry and Obama. Really strange.
These were generally traditionally Democratic areas (though a little less so in Carter). However, all three voted for Clinton twice and Dukakis. Bath was Democratic in every race from 1940 to 1996 with the exceptions of the 72 & 84 landslides, Magoffin was Democratic in every election from 76 to 96. Gun control probably hurt Gore in those areas in 2000, swung back a bit to its Democratic roots with Kerry in 2004 as Gun Control was less of an issue. In 2008, swung back to the GOP because well a black guy running for President in Kentucky. Hillary would have won all three, in fact she won the Primary in a landslide in all three (Bath 83%, Carter 87%, Magoffin 93%)
All in all though these areas didn't swing all that much. Some of the margins were very close. For example in Carter, Kerry only won by 1.39% in 2004. McCain only won Bath County by 0.53% for a grand total of a 24 vote margin. Magoffin was won by Kerry by 0.12% (7 votes).
So two of the Kerry victories, as well as one of the McCain victories were by very small margins. The margins in all three counties were in the single digits for all three elections.