Does ProsperOps work with container services like EKS and ECS?

Yes. ECS has two delivery modes: one that uses EC2 and one that leverages Fargate (which abstracts EC2 instances away). EKS, at present, is only delivered with EC2. RIs apply in both EC2 delivery models and RI discounts should be a significant (but not the only) factor when considering EC2 vs. Fargate.