This question is kind of correct - it is just very informal. In a formal setting, it should be "Is Khamenei another Khomeini?" And Mohsen, I am afraid you have totally confused everyone by the background information you gave in brackets - just because it should be "Khamenei and Khomeini are male names."

The sentence could be correct in another context but as it is, it's too vague. Khamenei is another khomeini? ( khamenei and khomeini is male name) As I read both sentences I believe you are trying to say this: Khamenei and Khomeini are similar and both are male names. ?????

This sentence is completely wrong.

Khamenei and Khomeini are males names.