Many, many land disputes between States have either been settled by negotiation or by a Supreme Court decision. Wikipedia has entries covering 45 of them. Most large disputed areas had been settled in favor of one colony or another prior to American independence, but others involving the original colonies' land claims west of the Appalachians were settled by the Continental Congress or the Supreme Court after 1789. Mark Stein's book How the States Got Their Shapes is an entertaining examination of many of these disputes. His followup book, How the States Got Their Shapes Too: The People Behind the Borderlines, tells the stories of some of the smaller pre-Revolutionary disputes by focusing on the personalities involved.
One of the more famous 19th century disputes involved Greer County, Texas. Confusion resulting from an inaccurate map and ambiguity about various forks of the Red River meant that Texas claimed 2300 square miles that the Supreme Court ruled instead should be part of Oklahoma (not yet a state). Even within the last three decades, the Supreme Court has decided disputes regarding the Ohio-Kentucky border and whether New York or New Jersey has jurisdiction over Ellis Island.
Michigan and Ohio had a dispute over a slice of land called the Toledo Strip in what is called the Toledo War. It concerned the strip of land in what is now northen Ohio, but was controlled by Michigan when Ohio claimed it.