Which one is better or which is better?
Either one could be correct, depending on the context. Although they are both correct, using 'which is better' is the preferred choice. If you are looking for multiple answers to the question in which you ask this, I suggest using 'which are better' instead.
Which is the best or better of the two?
Better of two is correct. Best is used when the comparison is among more than two persons.
Which is correct or which one is correct?
But consider this: the is in X is is only correct if X is singular. So the one can be omitted - but you can always say which one to emphasize if the listener/reader might not be paying attention or you otherwise want to be really clear.