Can someone tell us which one is the better choice and list some pro/cons?
For games -> .tmx?
for other reasons -> SKTileMapNode?
If you see the JSTileMap ReadMe page on GitHub it recommends to use SKTilemapNode. This is a clear indication of a direction to follow.
JSTileMap is written in Objective-C and seems like no intention to port to Swift exists, that would be enough of a reason to choose SKTilemapNode.