I want to create one kubernetes cluster on GCE and another one on AWS, both running the same application.
What would be the best way to load balance across them?
You can deploy the same application on both platforms, expose it via an L3 / L7 service and then create a DNS entry that includes the public IP for each cluster.
If you want more than just round-robin load balancing, you can use a service like Route 53 to do latency or geo based routing and also add DNS health checks.