What a conundrum. If you want a battle between uniformed soldiers, which took place during Morgan's Raid, the northernmost battle is Salineville, Ohio.
If you want a bank robbery by 22 Confederates in civilian clothes, you get the St. Alban's Vt Raid where no uniformed soldiers of either side were present, and the only one killed was a St. Alban's resident who was a Southern sympathizer.
The St. Albans Raid in Vermont is defined as as land action, not a battle, on Wikipedia, so I'm going with the Battle of Killdeer Mountain in the Dakotas (later North Dakota). There are five Civil War Battlefields in North Dakota, as defined by the Civil War Sites Advisory Commission established by Congress in 1990 and Killdeer Mountain appears to be the northernmost. http://blog.statemuseum.nd.gov/blog/civil-war-north-dakota
The Raid on Saint Albans, Vermont. I used to room with a girl from there when I was at Florida State. We kept asking the intramural guy if we could get an ice hockey team together, but he never obliged us.