The best way would be is to have 1 kubernetes cluster and have the worker nodes in private subnets. You can choose to have the control plane in a public subnet with restricted access like your VPN cidr etc.
If you have multiple teams or application stacks, I'd suggest having different namespaces for each stack as this creates the logical separation of resources.
Also, check the resource limits and quotas that you can apply on kubernetes to prevent over consumption of the resources.
And, as you mentioned multiple application stacks, I am assuming you would have multiple services being exposed for each application or something similar. I would highly recommend using a ingress controller (nginx or anything) to work as single point of entry for each application. You can have more than 1 application listening to 1 load balancer.
Also, have prometheus or ELK monitoring in place as they are great with monitoring k8s components and metrics.
And, I would highly recommend using a tool kubecost and kubebench for enhancing your k8s cluster.
Kubecost is for cost analytics and reporting for k8s components and kubebench would audit your cluster against CIS standards and give you a report on what improvements are required and where.
Please note that the above recommendations are based on best practises and cost efficiency.