What does it mean bipolar or unipolar junction in a transistor?
No, you're reading it wrong. Both 'Bipolar' and 'junction' are not "connected"... I mean to say it is not like junction is bipolar or unipolar. Actually 'Bipolar' means current conduction in device is due to both polarity charge carriers, electrons and holes. In NPN BJT, electrons are majority charge carriers and holes are minority charge carriers but holes still play their (small) part in conduction hence called bipolar transistor. FETs in which only one, either electrons or hole plays part in current conduction are called 'Unipolar' transistors 

I haven't heard "Unipolar junction" term but if you are referring to UJTs then
'UniJunction' word signifies that the device has only one P-N junction and not that the current conduction is due to only one type of charge carriers, however that's true.