I agree with bullgatortail, at least to some extent. The Saint Alban's battle is the northernmost battle I've ever seen reference to.
However, it appears that the National Park Service, at least, doesn't recognize that as a battle. It has some Indian battles that occurred during the Civil War as far north as Idaho (my point being that it's not just listing the big battles that everyone's heard of, but it doesn't list any in Vermont. The farthest north of the battles it lists appears to be Gettysburg.
So... who knows. The first link below sure sounds like it's for real, but I dont' see why it wouldn't be acknowledged on the battlefields site. Maybe because it was in town?
The northernmost battle of the Civil War was fought in St. Albans, Vermont, on October 19, 1864. A group of 22 Confederate soldiers, led by Lt. Bennet H. Young, crossed from Canada into St. Albans, shot up the town, and robbed three banks of more than $200,000. They attempted to burn the village, but townspeople prevented this destruction. Eleven members of the group escaped back into Canada where they were arrested and later released.
The northernmost naval engagement was the Battle of Portland, Maine, on June 27, 1863. There were two fights in Ohio--the Battles of Buffington's Island and Salineville.
On a grander scale, the Battle of Gettysburg (Pennsylvania) was the northernmost major engagement. There were several battles in Maryland (Antietam, Monocacy, South Mountain, Crampton's Gap), and the Battle of Fort Stevens was fought within the District of Columbia.
(from The Civil War Day By Day)