How to check if VPC gateway endpoint being used or NAT gateway is used

You can check the communication path using "Reachability Analyzer"
In addition, if you check CloudTrail after executing an API such as "aws s3 ls" from EC2, there is a field called "vpcEndpointId", so you can check from there.

When setting up an interface VPC Endpoint to access an AWS Service privately from within a VPC, the endpoint will 'hijack' the traffic to use the local endpoint you placed rather than the public ones. A quick way to verify this from an EC2 instance in your VPC is to SSH into it and do an NSLOOKUP on the endpoint (i.e. nslookup ec2.us-east-2-amazonaws.com - adjust accordingly). If it returns an address from the VPC's address range - you are using the endpoint. If it returns a public IP address then you will use the public endpoint. Here is an article to troubleshoot if it is not working - https://repost.aws/knowledge-center/vpc-interface-configure-dns.