For harmony: I heard "Theory of harmony" by Schönberg is pretty good. It's the only book about harmony I have so I don't really have a comparison, though I did some research on which book to buy before ofc.
Anyway, if you take your time with this one - and I mean lots of time - you're sure to get a vast knowledge of harmony.
Warning: at times he keeps on philosophizing about certain topics, which can be interesting to read but quite a bore aswell.
(And don't worry, it's not about 12-tone or serial music or any such thing)
For counterpoint: I have Kent Keenan's "Counterpoint", again the only book on the subject I read, so no comparison. However I heard it's pretty good (haven't read too far into it yet myself) so I'll just blindly hand the suggestion on to you. Again, you'll need to take your time and make sure you get everything before you move to the next chapter, otherwise things will become very puzzling very quickly.
For Orchestration: I don't know but apparently it's very important for composing.

I think this is also the order in which you should study music theory:
Harmony - Counterpoint - Orchestration
Good luck
