None of those words are "bad" words but admittedly, I hate the word fart. I just don't like it. It sounds crude and vulgar so I have never encouraged that word and have always discouraged it by saying, "toot." I think it sounds better. Or a gas bubble in the tummy sounds more accurate.
As for pee and poop and butt, they are decent words. There are other words I've heard parents call poop and honestly, those words sound just as vulgar. It all comes down to what makes you feel comfortable and what words you find yourself saying because whatever words they are, trust me, the kiddos will repeat them. If your child repeatedly says a word or phrase you dislike, tell your child that the word sounds bad and instead offer a substitute word for that word instead. I hope this helps.