Emphasis added:
Please see Scammer abusing your SSL Certificate - #2 by _az and The CA's Role in Fighting Phishing and Malware
I'm sure if a US court asks for the revocation, Let's Encrypt will obey. But without an official judgment, it's hard to define "clearly used for criminal activities". Furthermore, the certificate provided by Let's Encrypt only says that you are contacting the owner of the website, nothing more. Asking the registrar or the hosting provider is in my opinion a better legal course of action.