Using Amazon VPC provided DNS trough AWS Site-to-Site VPN
Is it possible to query Amazon DNS server from our corporate network trough the VPN tunnel?


Directly? No. The recursive resolver available by default when you create a VPC can only be accessed by an IP address in that VPC. This is a restriction that Amazon imposes.

What you can do is create a forwarder using the Route 53 Resolver service or software like Unbound. You can then (conditionally) forward your onprem DNS for certain domains to it.

Some useful links:

https://docs.aws.amazon.com/vpc/latest/userguide/VPC_DHCP_Options.html#AmazonDNS

https://docs.aws.amazon.com/vpc/latest/userguide/vpc-dns.html#vpc-dns-support

https://docs.aws.amazon.com/Route53/latest/DeveloperGuide/resolver.html