Is my book too similar to Harry Potter? How can I make it less similar?

There are similarities and it might be too many. Better that you realize now rather than later.

Note: I am a lawyer (retired) but I'm not your lawyer. So if you want a confirmation of my advice and to get better protection against a potential copyright case, please consult with a competent legal professional in your area.

A mean boy in a teen situation is one of what's called scènes à faire. The concept is that some scenes or scenarios or characters are so standard in a particular genre that they are expected by the reader/viewer and cannot be copyrighted. Such as a kiss in a romance (or an elopement, an objecting parent or friend, an ex, etc.), a gunfight in a western (or a posse, a hanging, a saloon, etc.), or a ray gun or something like it in space opera-style science fiction (or a space ship of some sort). So I'd say you're okay with him but make his name as far away from Draco as possible. Not Dan, Dave, Don, etc. More like Zach or Luis or the like.

A magic school isn't so much a scène à faire but you are probably okay as it's been used in other places than Harry Potter (it was a big plot point in some of the middle seasons of the Charmed TV show). But you might want to expand it and refer to it more as a magic school than a school specifically for wizards.

The book of destiny is a pretty standard fantasy trope. Harry Potter had the philosopher's stone; Charmed had the book of shadows. Same diff. So you're probably okay so long as you don't copy whole swaths out of either.

The name for the normal folks is probably okay but again keep the sound far away from the word muggle.

Best of luck with your writing!

Your book in no more similar to HP than any number of YA fiction series. Both HP and your outlined series use common tropes of adolescent life, schools, bullies, etc. It's no big deal. I remember when my wife was reading the first Twilight book. I asked her when the werewolves were coming because just about every series with vampires in it introduces werewolves as a foil. Sure enough, here comes the werewolves. It's part of the genre.