You can do something like this with the MIMEEntity. Then you will be able to stream an attachment right into your notesdocument. You will have to get a handle to a notesdocument and an outputstream with the file content. Then you can try to do something like I have done in the code snippet here.
MIMEEntity m = newDoc.createMIMEEntity( fieldNameForFiles );
MIMEHeader header = m.createHeader("content-disposition");
header.setHeaderVal("attachment;filename=\"" + this.getFileName() + "\"");
Stream oStream = session.createStream();
InputStream is = new ByteArrayInputStream( ((ByteArrayOutputStream)outStream).toByteArray() );
oStream.setContents(is);
m.setContentFromBytes(oStream, "application/pdf", MIMEEntity.ENC_IDENTITY_BINARY);
m.decodeContent();
newDoc.save(true, true);