I remember one great article in particular dismantling common misconceptions about medieval times.
Any good academic sources, preferably articles, against the idea of dark ages would be much appreciated
Basically, Western Europe was not the entire world. Western Europe just calls it the Dark ages because they want to pretend the entire world was retarded for the period, not just Western Europe, because Western Europe likes to pretend it was the greatest for all of history.
Regardless of any popular misconceptions about the dark ages we do know one thing for certain. And that's the depopulation of urban areas. That phenomenon alone explains much of the other trends in the era.
Also, James Franklin has a few articles talking about the Middle Ages here: http://web.maths.unsw.edu.au/~jim/medmyths.html and about the Renaissance here: http://web.maths.unsw.edu.au/~jim/renaissance.html
Thony Cristie is another historian. He has a blog where he posts about History of Science in the Renaissance and reviews books by other historians of science. He has appeared insome interviews and has given some talks as well.