I understand this is a subjective question, so I apologize if it needs to be closed, but I feel like it comes up often enough for me to wonder if there is a general preferen
I prefer the second option, the if (value == false) one.
I gladly use if (~value) or if (not value) in languages that support it, but that ! just merges waaaaay too easily either with the variable name or opening braces or | or || operators... at least in my opinion.
Also, two things:
if (value == true), and I'm aware I'm inconsistent. And although consistency is very important in my opinion, that pesky ! is simply worse.