byte in Java is 8 bit signed. So you will get negative values.

Change

System.out.println(s[i]);

to

System.out.println(s[i]&0xff);

to get the same values.

Update: I just saw that Java 8 introduced Byte.toUnsignedInt(). This is perhaps more readable:

System.out.println(Byte.toUnsignedInt(s[i]));

As of Java 8, there is an officially supported API for Base64 encoding and decoding. In time this will probably become the default choice.

The API includes the class java.util.Base64 and its nested classes. It supports three different flavors: basic, URL safe, and MIME.

Sample code using the "basic" encoding:

import java.util.Base64;

byte[] bytes = "Hello, World!".getBytes("UTF-8");
String encoded = Base64.getEncoder().encodeToString(bytes);
byte[] decoded = Base64.getDecoder().decode(encoded);
String decodedStr = new String(decoded, StandardCharsets.UTF_8);

The documentation for java.util.Base64 includes several more methods for configuring encoders and decoders, and for using different classes as inputs and outputs (byte arrays, strings, ByteBuffers, java.io streams).