I have written a program in .NET framework 4.5 to encode and decode a binary or text file to and from base64. To make the conversion I use the methods ToBase64String and FromBase64String from the System.IO Namespace.

The compiled file: base64.zip (You will need .NET framework 4.5 to run it).
The source file: base64.cs

Syntax: base64 [-e / -d / -encode / -decode] <input file> <output file>

Example:
base64 -encode test.bin test.b64
base64 -decode test.b64 test.bin