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In addition to @Francesco Pitzalis's answer...

String concatenation

String result = new String();

This is never required as Strings are immutable in Java. If you find yourself using it to append String values, then you should be using StringBuilder (the faster, non-synchronized version of StringBuffer, which is usually recommended unless you require the multi-threading safety of the latter):

StringBuilder result = new StringBuilder();
// ...
result.append(integer % 2); // add some spaces for readability
// ...
return result.reverse().toString();

try-with-resources

// don't forget to close the Scanner
inputScanner.close();

Since you are on Java 7 at least (from the use of String in switch), you should be using try-with-resources to safely and efficiently manage the underlying I/O resource used by your Scanner instance:

try (Scanner scanner = new Scanner(System.in)) {
 // ...
}

Choices and enums

On a related note to your isDecimalOrBinary() method (which @Francesco Pitzalis's answer made a very good point), the return type can also be modeled as an enum should you still choose to keep it:

enum ValueType {
 DECIMAL, BINARY;
 public static ValueType parse(String value) {
 // ...
 }
}

This eliminates the possibility of typos in your expected String return values, e.g. when you return "decimal" but are wrongly checking for "Decimal" from calling the method.