Before we deal with style, let's consider the substance.  I don't think that the following code leads to unbiased sampling as you intend:

    for(; ; i++){ 
        int randomIndex = (int)(Math.random()*(i + 1));
        if(randomIndex < sampleSize){
            sample[randomIndex] = StdIn.readString();
        }
    }

That raises the issue, are you not able to reuse the classes already developed from your previous exercise?  In software development, it would be much preferable to call existing code than to reimplement an algorithm using copy-and-paste.  Had you done so, this sampling error would have been avoided completely.

Next, I question your statement
> All the code is inside the main() because that is how the api demands it.

As I [commented in the previous exercise](https://codereview.stackexchange.com/questions/30764/review-of-reservoir-sampling?lq=1#comment49017_30808), the API demands that your `main()` take a single string parameter that will be parsed as an integer representing the number of samples to take, out of the pool of data that will be read from standard input.  The API does not demand that all of your code live inside `main()`.  (Your *instructor* might demand it, but that would just be silly, in my opinion.)

To address your specific question of flow control, catching `RuntimeException` is a horrible idea.  It's much too unspecific; who knows what kind of `RuntimeException` actually triggered the premature termination of your loop?  Furthermore, it's unclear to anyone looking at the code that it is the intended behaviour; exceptions (especially `RuntimeException`s) usually signify for unexpected events.  Let's face it, you're catching `RuntimeException` instead of `NoSuchElementException` to work around the silly artificial constraint of your exercise that you must not use anything outside `java.lang.*`.

The correct way to detect the end of input from `java.util.Scanner` is to call `Scanner.hasNext()`, and the next best way is to catch `NoSuchElementException`.  If both of those options are artificially closed off from you, then your question is dangerously close to being [off-topic](https://codereview.stackexchange.com/help/on-topic) for this site, as it would violate the "Do I want the code to be good code" rule.