Raw data will be transferred from the source through an HandleHttpRequest. How can I encrypt in motion this traffic?
You will need to send the raw data to NiFi HandleHTTPRequest using https protocol. This will require that NIFI be secured (per required documentation). If your source is secure also, the HandleHTTPRequest should be configured using an SSLContextService with a keystore and truststore containing the certs for the source.
You will need to configure your HandleHttpRequest processor with a SSL Context Service in order to encrypt data in transit being sent to this processor from a client. This of course then means you client needs to be able to at a minimum to trust the server certificate presented by this SSL context service in the TLS handshake. The truststore you use in the NiFi SSL Context Service will only need to contain the public cert for your client or complete certificate trust chain for your client if you have configured your HandleHttpRequest processor to "Need authentication" in the Client Authentication property. Mutual Authentication is not needed to ensure encryption of data in transit.
Hope this helps,