Instead of (بجای)- I would like some tea instead of coffee.

In place of - another way to express something being replaced, for e.g. dancer A will perform in place of dancer B (this is usually used with something has happened to the original subject that now can't be used).

Rather than - similar to instead of, for eg I would like to see you rathen than him, taking the bus is cheaper rather than faster, etc.

My destination is A city instead of (rather than) B city

I will request a substitute teacher to lecture in place of me on this weekend.