If line terminators are always one or the other, I would suggest setting up 2 file connection managers, one with a CRLF line separator and the other with an LF line separator.
Then create a variable of type boolean (something like @IsCrLf) and apply it to your package. Take the first step in your SSIS Script package The task in which you read in a file stream and try to figure out what the line terminator means (based on what you find in the stream). Set the value of your variable accordingly.
Then after the Script task in your control stream, create 2 separate data streams (one for each file connection manager) and use Precedence Constraint set to “connectors” and “Expression and Constraint” to indicate which data stream to use, depending on values of the @IsCrLf variable.
An example of a suggested control flow is below.

GShenanigan
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