The three most popular DNS protocols with transit encryption are DNS-over-HTTPS (DoH), DNS-over-TLS (DoT), and DNS-over-QUIC (DoQ). This should help you choose what to use:
- Do you actually need to override OS DNS support? If not, or if you’re unsure, go to 6.
- Are you ready to implement DNS protocols correctly, or add a dependency that does so? If you’re not, go to 5.
- Does the network filter DNS traffic? If it does, go to 5.
- Do you already have QUIC support? If not, use DoT. If you do, use DoQ.
- Do you have an HTTPS stack? If you do, use DoH.
- Give up and delegate to the OS.
Let your HTTPS stack handle HTTP/1.1 vs. HTTP/2 vs. HTTP/3 support; don’t treat DNS-over-HTTP/3 as a separate protocol. I don’t know enough about DNSCrypt to make an informed recommendation about it, but DoQ and DoH meet my needs well enough.