Making sure user inputs correct type
If the user is non-technical they may not know what an integer is, but
  I can't think of better wording.


[Positive] Number or [Positive] Whole Number would be alternatives. 

Another possibility: Enter a Number between 0 and [X]. Non-technical people will assume that this means they should enter a whole number. If they enter a different number, give feedback accordingly.

Consistency

In your first version: getNumber outputs the prompt each time, while getBool does not. This should be consistent. The names of the input variable should be consistent as well (either prompt or message. I would prefer prompt.

Other

You can do sc.nextInt(); instead of String input = sc.next(); Integer.parseInt(input);.

As already mentioned on UX, show the possible values for the boolean answer in the prompt when asking the question. So 

boolean wind = getBool("Regularly windy"); 


becomes

boolean wind = getBool("Regularly windy (y/n)"); 


Extract Method

You can extract the method to retrieve a string. I think that this makes the code a bit more readable, and you get getString method for free.

/*returns integer to question asked in prompt*/
public static int getNumber(String prompt) {
    while (true) {
        String input = getString(prompt);
        try {
            return Integer.parseInt(input);
        } catch (NumberFormatException ne) {
            System.out.println("\tPlease enter a positive whole number.");
        }
    }
}

/*returns boolean to question asked in prompt*/
public static boolean getBool(String prompt) {
    while (true) {            
        String input = getString(prompt).trim().toLowerCase();
        if (input.equals("y")) {
            return true;
        } else if (input.equals("n")) {
            return false;
        } else {
            System.out.print("\tPlease answer y/n");
        }
    }
}

/*returns string to question asked in prompt*/
public static String getString(String prompt) {
    System.out.print("\t" + prompt + ": ");
    Scanner sc = new Scanner(System.in);
    return sc.nextLine();
}