How to mention a recently dead scientist? I would like to mention in an article a scientist that passed away in 2015 and was universally recognized as a pioneer in his respective field. Since many knew him personnally, I would like to mention him respectfully, such as 'the Late Dr. XXX' or 'Honorable Dr. XXX'.

I am afraid it would be unethical, especially considering that many other authors that I mention are also gone (but few people really knew them) ?
I would strongly advise you against that idea. A well written article has to remain objective. Your relationship with that scientist is not a matter of any importance in the research you are describing in the article. Even adding qualifiers to the name is a bad move in my opinion, as you would be imposing your judgement to the reader. 

I know this might seem a nice gesture in the moment, but the article is here to (hopefully) stay, and this type of personal/temporal address will become even more irrelevant to the reader.