As of today, CodeDeploy doesn't support cross-account deployments. Depending on what your goal is, you might be able to achieve it another way.
I want to deploy a bundle in one account to another account
If your S3 bucket allows access to the second account, CodeDeploy doesn't care what account your bundle is in as long as everything can access it. Per @TimB, it looks like CodePipelines can support that behavior.
I need to initiate a deployment in one account to another
If you have a reason why the deployment must be in one account to another, you could set up the instances in the second account to be on-premise instances, though this is not a great solution.