"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."
In light of of the comment I received, I need to add an edit to my statement above.
When you say: "he is one of my favorite scientists," you are expressing your current feelings stimulated by the existence of a particular scientist. If you shift this into the past and say: "he was one of my favorite scientists," you could either be expressing that the stimulus for your feelings no longer exists (e.g., the scientist has died or has changed professions) or that your feelings have changed despite the fact that the stimulus may still exist.
The default is to associate the stimulus with the person per se; however, in an appropriate context, the stimulus could be the person's work or legacy or accounts of what the person has achieved.
It would be natural for someone to say: "My favorite scientist is Isaac Newton; his theories are still quite relevant." It is also natural to say: "Plato is my favorite philosophyer." An elderly person could also say, "Einstein was my favorite scientist," implying that he was alive during the person's lifetime and that they are remembering him during his life.
It would also be natural for an elderly person discussing their studies when while young and at university to say: "My favorite scientist was Isaac Newton," implying that they are talking about the time during their studies and not their current feelings. An elderly person could also say, "Einstein is my favorite scientist" and imply that they are referring to their ongoing exposure to his legacy, work, or descriptions and not the living individual.
In the posted question, it is the scientist as a live individual that is being discussed, which calls for the past tense after his death.
Out of context, if I said: "he was one of my favorite scientists," it is ambiguous whether I am saying that he is no longer a favorite or that he is no longer a current scientist because of death or some other reason.