I've never worked with a Nexus 6K, but a couple of things I'd check:
1) If it's a L2 port channel, it will only support an L2 flow config. It will be something like "layer2-switched monitor ....". If it's a L3 port channel, you should be able to configure a L3 flow monitor.
2) Make sure you're running recent code that has full NetFlow support. NetFlow support on Nexus platforms has historically been all over the map.