You can use a Scanner
then use Scanner.nextLine();
to get input from the user in the console.
Also, you may want to take a look at the standard naming schemas in Java
Scanner scan = new Scanner(System. in ); //Create a new Scanner
System.out.println("Would you like the average, or sum?");
String input = scan.nextLine(); //Get input from the user
int SumChocolates = 0; //Must declare out here, because Average case uses this
SumChocolates = (int)(data[0][7] + data[1][7] + data[2][7] + data[3][7]);
if (input.equalsIgnoreCase("Sum")) {
System.out.println("The Sum is: " + SumChocolates);
} else if (input.equalsIgnoreCase("Average")) {
int AvgChocolates = 0;
AvgChocolates = (int)(SumChocolates / 4);
System.out.println("The average is: " + AvgChocolates);
}