How to get Java to wait for user Input

There is no need for you to check for available input waiting and sleeping until there is since Scanner.nextLine() will block until a line is available.

Have a look at this example I wrote to demonstrate it:

public class ScannerTest {

    public static void main(String[] args) {
        Scanner scanner = new Scanner(System.in);
        try {
            while (true) {
                System.out.println("Please input a line");
                long then = System.currentTimeMillis();
                String line = scanner.nextLine();
                long now = System.currentTimeMillis();
                System.out.printf("Waited %.3fs for user input%n", (now - then) / 1000d);
                System.out.printf("User input was: %s%n", line);
            }
        } catch(IllegalStateException | NoSuchElementException e) {
            // System.in has been closed
            System.out.println("System.in was closed; exiting");
        }
    }
}

Please input a line
hello
Waited 1.892s for user input
User input was: hello
Please input a line
^D
System.in was closed; exiting

So all you have to do is to use Scanner.nextLine() and your app will wait until the user has entered a newline. You also don't want to define your Scanner inside the loop and close it since you're going to use it again in the next iteration:

Scanner userInput = new Scanner(System.in);
while(true) {
        System.out.println("Ready for a new command sir.");

        String input = userInput.nextLine();
        System.out.println("input is '" + input + "'");

        if (!input.isEmpty()) {
            // Handle input
        }
    }
}