Специальные символы Java заменяют

Вам необходимо использовать MimeUtility. Вот пример.

public class Mime {
    public static void main(String[] args) throws MessagingException,
            IOException {
        InputStream stringStream = new FileInputStream("mime");
        InputStream output = MimeUtility.decode(stringStream,
                "quoted-printable");
        System.out.println(convertStreamToString(output));
    }

    public static String convertStreamToString(InputStream is)
            throws IOException {
        /*
         * To convert the InputStream to String we use the Reader.read(char[]
         * buffer) method. We iterate until the Reader return -1 which means
         * there's no more data to read. We use the StringWriter class to
         * produce the string.
         */
        if (is != null) {
            Writer writer = new StringWriter();

            char[] buffer = new char[1024];
            try {
                Reader reader = new BufferedReader(new InputStreamReader(is,
                        "ISO8859_1"));
                int n;
                while ((n = reader.read(buffer)) != -1) {
                    writer.write(buffer, 0, n);
                }
            } finally {
                is.close();
            }
            return writer.toString();
        } else {
            return "";
        }
    }
}

Файл 'mime' содержит закодированный текст:

Csukl=E1si roham gy=F6t=F6rheti a sv=E9deket, annyit emlegetik mostans=E1g =
ism=E9t a
sv=E9d modellt Magyarorsz=E1gon.

ОБНОВЛЕНИЕ:

Использование библиотеки Guava:

    InputSupplier<InputStream> supplier = new InputSupplier<InputStream>() {
        @Override
        public InputStream getInput() throws IOException {
            InputStream inStream = new FileInputStream("mime");
            InputStream decodedStream=null;
            try {
                decodedStream = MimeUtility.decode(inStream,
                "quoted-printable");
            } catch (MessagingException e) {
                e.printStackTrace();
            }
            return decodedStream;
        }
    };
    InputSupplier<InputStreamReader> result = CharStreams
    .newReaderSupplier(supplier, Charsets.ISO_8859_1);
    String ans = CharStreams.toString(result);
    System.out.println(ans);