The ACME standard (and TLS-ALPN-01 draft) and Let’s Encrypt just use the standard DNS, HTTP and HTTPS ports – 53, 80 and 443.
(I’m not sure it explicitly says to make DNS queries using port 53, but it’s implied at least.)
The Baseline Requirements also allow CAs to use the standard SSH and mail ports, but Let’s Encrypt doesn’t do anything with them.