I'm not exactly sure how your transform is calling the base64 encoding function, but the Base64Encode method from the %System.Encryption class does this by default.

classmethod Base64Encode(Text As %String, Flags As %Integer = 0) as %String

Input parameter: 
Text - String to be encoded
Flags - 0 - Insert CR/LF after every 76 characters (Default)
Flags - 1 - Do not insert CR/LF after every 76 characters.

You would need to override the default flag to not insert line breaks.