Literally Are you that? If this is right, then clearly Czech looks at things differently. English Is that you? focuses on that, making it the subject of the sentence and leaving you as the subjective complement. Czech, in contrast, focuses on the person, putting him or her centre stage, so you get That - are you? equivalent to Are you that thing?, whereas English asks Is that thing you?
english "Is that YOU?" or "You are THAT?" or "You ARE that?" with stress on the capitalised word would all be "To jsi ty?" in Czech, you would just but stress on the word you would like to point out. "TO jsi ty?" x "To JSI ty?" x "To jsi TY?". It is really a matter of speech.
Jsi to ty? or Jste to vy? are also correct translations. The meaning of To jsi ty? And Jsi to ty is slightly different.
When you ask "To jsi ty?" - It says that you are surprised for example that the person on some old photo is really your friend. (You just can't recognize him and you ask to be sure.)
When you ask "Jsi to ty?" - you use this when you don't see the person and want to make sure that the person is the right one you are waiting for. For example when someone knocks on your door.
Are i and y pronounced the same or is there a difference that I cannot hear?
There is no difference between i and y, they are pronounced the same. However, there is a slight difference in pronounciation of the short i/y and the long í/ý (but most native speakers are not aware of it):
i/y = [ɪ]
í/ý = [iː]