Is it appropriate to email a professor saying you enjoyed their class, after doing well in it?
As my experience of being a TA for multiple courses with various profs, such personal gestures of appreciation are welcomed by the professors. I have actually heard professors refer to the email as something that "made their day". As long as you don't refer to your grades, I don't see a reason why someone would misjudge your intentions, especially after the course has finished.
Email the professor, they are human too, they like hearing that you enjoyed their class.
1) I...said this in the class evaluations, which the prof will read.
Class evaluations are presumably anonymous, an email from you is more personal.
2) More importantly, I recently received my final grade and it was good...If I email now, it might come off as an implied "thank you" for giving me a good mark...
You've done well because of your hard work, the professor hasn't done you any favours. (Regardless, if the class is sufficiently large, then the professor won't remember your grade and is surely unlikely to go to the trouble of looking it up.)
I will just throw in my personal experience about this subject. Three years ago I was taking an undergraduate course with a great professor. I was at a point where I didn't want to continue studying (I won't go deep in this subject), and he changed my mind just by the way he was teaching. He always gave more than he needed to, always pushed us forward and had a great way of teaching.
Half way through the semester, I asked for a meeting with him during the office hours to ask about a subject in his course. He answered all my questions and gave me more than he had to.
At the end of the semester, and after getting all my grades I decided to email him because I wanted to thank him for such a nice semester I had with him and for all the push he gave me to continue my studies.
He was so happy that I shared all the information with him because he didn't really know the impact he had on me. He invited me to his office and we had some discussions not regarding the studies. He even asked me to stay in touch (we're still in touch).
A professor might not always know the effect he had on his students, and he would like to get all the feedback possible (Class evaluations are not enough IMO). It's always good to give a push and a "Keep going" sign for a good person.
Bottom line:
Yes, it is appropriate to thank a human being for their effort, being it a professor, a doctor, a stranger you met on the road. It's just a nice and good gesture of you and it will surely make them happy. Believe it or not, it will.