I think with "have always thought" I'd normally use "is" if the guy is still alive. I'd use "was" if the guy was, for example, a historical figure, who has not been alive during my lifetime, or not since my childhood maybe. The idea is that I have "always" (which might not be quite literally "always" but just "for a long time") had that opinion, which has always been an opinion (expressed in the past tense, "was") about someone who is no longer alive. I don't think we'd use "has been" as per your 3rd example, thought we might with some added words, such as "when it has suited him" (though "is"..."when it suits him" is probably more likely). For someone who is no longer alive but was until recently, you might say "I always thought he was a good guy". You'd use the same construction if you have changed your opinion - "I always thought he was a good guy, until I saw how he treated his girlfriend".

All three make sense. #1 and #2 have almost the same meaning. In #1, "he is a good guy" is a timeless truth. The present tense doesn't necessarily establish any time frame. #1 only makes sense if he is alive. #2 opens up the possibility that he might not be a good guy. It also opens up the possibility that he might be dead. However, neither of those needs to apply. The source of your confusion in #3 is the so-called "present-perfect tense" and its interpretation as action starting in the past and continuing into the present. That is what is written in textbooks and it is sort of true, but not completely true. You will understand #3 better if you forget about that tense and concentrate instead on the meaning of the words "has" and "been". Think of "been" as a noun that means "experience of being". "He has been a good guy" means "He has experience of being a good guy". It is present tense! You can use it in #3 just as the present tense is used in #1 to represent a timeless truth. "He has been a good guy" is a timeless truth. You have always thought so.

The 2nd seems most natural to me. I can't quite explain why the tenses work that way. It sounds past, but basically means it started in the past and continues into the present.