I would go with x.equals(y) because that's consistent way to check equality for all classes.
As far as performance goes, equals is actually more expensive because it ends up calling intValue().
EDIT: You should avoid autoboxing in most cases. It can get really confusing, especially the author doesn't know what he was doing. You can try this code and you will be surprised by the result;
Integer a = 128;
Integer b = 128;
System.out.println(a==b);