Firstly your isLeapYear condition needs to change.
boolean isLeapYear = ((Year % 4 == 0) && (Year % 100 != 0) || (Year % 400 == 0));
Next your if(TwentyEight.contains(Month)) for this need to change to consider leap year.
if(TwentyEight.contains(Month) && !isLeapYear) {
System.out.println(Month + " " + Year + " has " + DaysTwentyEight
+ " days in it.");
}