Is it well-received to thank the assignment author at the end of a course?
Yes, I think it would be fine. Everybody likes to know their work is appreciated. Teaching assistants are often not appreciated enough  by their students (and sometimes not enough by their professors!).

Just a short concise form of thanks would be enough:


  Thanks for those exercises you set for course xyz. They were really interesting, and I enjoyed solving them. I hope you liked creating them as much as I appreciated their contents.


Something along those lines perhaps. If you make it too long it might sound obsequious or sycophantic.