Kinnaur is located at Sangla valley that faces Chitkul where you get to see lovely mount Kailash. Located on the way to Tibet, Kinnaur is a land of temples, filled with apples to taste. Treks and camps are popular here. Manali on the other hand is a paradise spot of Himachal located between Pir Panjal and Dhauladhar ranges. Almost all through the year travel proves lovely to this ever honeymoon spot. Kinnaur and Manali are 11 hours apart. My suggestion would be definitely Manali for its nature, beautiful spots, and awesome peaks. Someday you should plan a separate trip to Kinnaur too.
Kinnaur is beautiful but limited no of activities and experiences though those available are extremely beautiful. Manali is a hub of activities and experiences most sought during travel. But if you haven't been to Manali then Manali is better option beyond doubt.