Based on this blog

Where should I setup the Alert Manager? Only for Central Cluster or each cluster has to be also alert manager?

What is the best practice alerting while using Federation?

The answer here would be to do that on each cluster.

If the data you need to do alerting is moved from one Prometheus to another then you've added an additional point of failure. This is particularly risky when WAN links such as the internet are involved. As far as is possible, you should try and push alerting as deep down the federation hierarchy as possible. For example an alert about a target being down should be setup on the Prometheus scraping that target, not a global Prometheus which could be several steps removed.

I though ı can use ingress controller to expose each prometheus server? What is the best practice to provide communication between prometheus server and federation in k8s?

I think that depends on use case, in each doc I checked they just use targets in scrape_configs.static_configs in the prometheus.yml

like here

scrape_configs:
  - job_name: 'federate'
    scrape_interval: 15s

    honor_labels: true
    metrics_path: '/federate'

    params:
      'match[]':
        - '{job="prometheus"}'
        - '{__name__=~"job:.*"}'

    static_configs:
      - targets:
        - 'source-prometheus-1:9090'
        - 'source-prometheus-2:9090'
        - 'source-prometheus-3:9090'

OR

like here

prometheus.yml:
    rule_files:
      - /etc/config/rules
      - /etc/config/alerts

    scrape_configs:
      - job_name: 'federate'
        scrape_interval: 15s

        honor_labels: true
        metrics_path: '/federate'

        params:
          'match[]':
            - '{job="prometheus"}'
            - '{__name__=~"job:.*"}'

        static_configs:
          - targets:
            - 'prometheus-server:80'

Additionally, worth to check how they did this in this tutorial, where they used helm to build central monitoring cluster with two prometheus servers on two clusters.