"He is one of my favorite scientists. He died a few years ago. He had
a nice sense of humor. One day, he threw a party for time travelers."
This is fine, but the use of "is" in the present tense is a little strange if the person is dead. Also, the last sentence is not well connected to the previous material. It would be easier to understand this sentence's connection to his humor if you said: "One day, he even went so far as to throw a party for time travelers," .
As for the past perfect, I think it is a very precise tense of last resort, when it is crucial to clarify the relative timing of events. Using it tends to destroy other nuances of English tenses. In this case, you have a simple past event, a lifelong state, and another past event. There is no need to add extra precision to mark the time sequencing. If you say: "He had had a good sense of humor," this suggests that something happened in his life to take away his sense of humor, such as an illness or a tragedy. It is obvious that death also does this, so there is no need to add the extra precision unless there is some other life event you want to mark the humor as being prior to.
Speaking of the dead, we tend to use the simple past tense to indicate habitual things or maybe a construction using "used to" to emphasize that something will no longer happen and may be missed. For instance, you could say:
"He was one of my favorite scientists. He died a few years ago. He had
a nice sense of humor and used to like to joke around. One day, he
even threw a party for time travelers."