Alright, this is a fun one. I need opinions from readers, not necessarily from authors.

My WIP has a few twists in it. At the moment (1st draft finished), the visible antagonist is just a thug, going on someone else's instructions. The thug is known to the reader (scenes even in his POV) and to the protagonist.
Currently, the ID of the thug's boss is not revealed (knife in back) to the reader or the protagonist until about 3/4 through, where it should come as a fairly major plot twist (he hopes).
Then, a little later, another twist is thrown in when it is revealed who was feeding the boss guy information (think knife being twisted here). Also a definite surprise (again, he hopes).
There is a further twist to the tale, but nothing to do with the identity of the antagonist, rather to do with the whole plot of the book.

Anyway, I digress. I have just read this little tidbit from some guy called Patrick Schulze.

A third way to take advantage of secrets is to enhance your climactic scene.How often have you read a novel where just as the hero is about to die, he learns a dramatic secret that changes everything and saves his life and sanity? Personally, I don’t care for this use. I think it was Orson Wells who said, and I paraphrase, terror isn’t terror unless the viewer knows something is about to happen. As I recall, he used the example of two people sitting at a table with a bomb underneath. There is much more suspense if everyone knows the bomb is there and are waiting for it to explode, than if it just detonates all of a sudden. I feel the same way about secrets. They have more power if everyone is waiting for the proverbial shoe to drop. Regardless my sentiments in this, a climactic secret might be useful to your story and you may wish to give it consideration.

Now I find myself wondering if I should reveal the boss' identity to readers early on, and let the suspense build to the revelation (penny drop) for protagonist) and just leave the other two surprises as surprises?

What do you prefer if you are reading? What is more 'fun'?

Having just read Stieg Larsson's The Girl with the Dragon Tattoo and The Girl who Played With Fire I don't see anything wrong with your original plan of revealing the chief antagonist 3/4 of the way in.
And it's always worth putting in a few other potential antagonists to throw the reader off the scent.

Declan,
I hope this won;t confuse you further but my children's novel to be published next year has a massive twist in it and I've had confusingly conflicting device about this issue! I paid for an editorial report from Cornerstones and the person who did it said I should foreshadow what was coming so it wasn't such a huge shock. Then an agent who was briefly interested echoed that, to the extent that she thought the twist should be in the title! I submitted directly to a children's indie publisher and they have taken it on but my editor there loves the twist and says I was to get rid of all clues.
So maybe it's a subjective thing after all..
Hope this hasn't been more of a hindrance than help. Good luck with the novel!

Hi Caroline. Thanks for your comments. It doesn't confuse me more, since it seems that I am heading in the direction of revealing one of those twists somewhat earlier. I hope that it will make the plot even stronger than it is with it as a surprise.

Good points Naomi. My wife just read both of these a few weeks back and agrees that the revelations were left to the right point. But I think with a crime/detective type story, it makes sense to leave that sort of revelation as long as possible too.

My surprise (the one in question) isn't so much a case of whodunnit, rather it is about the betrayal involved. The people recommending me to reveal that betrayal to the reader earlier on feel that it will build suspense as you wait for the protagonist to find out his friend is such a ...

I doubt there is a right answer to this, as Caroline's experience shows. But you can perhaps show that there's a bomb in the room, but not who put it there? The trick is to make sure that, from the reader's point of view, the table doesn't appear to just explode for no reason.

Yeah. Currently the bomb is clearly in the room. The choice I am making now is about when to have it explode.

It's a fun process to go through, but as I am reading the work as whole, I am getting more ideas about how to best execute the detonation of this particular bomb.