Both are frequently used, but I think "espere por mim" is more common.
Could you also translate this sentence as "I expect that he waits for me" ? :)
Or how about "I hope that he expects me" or "I hope he is expecting me"? Or is "expects" in the "knows I am coming" meaning a different word in Portuguese?
- I hope he is expecting me. Eu espero que ele esteja me esperando or Eu espero que ele esteja a me esperar
You could also say: Eu espero que ele esteja à minha espera. But I think this one is less common.
The meaning is close, but in Portuguese it would be: Eu espero que ele esteja me esperando.