Is it grammatically correct to say "I'm done with my apple pie" to indicate that you are finished eating it. I don't want to necessarily imply that I didn't like it.
It is grammatically correct, yes. It could mean either that you've eaten all of your apple pie ("I'm done with my apple pie; is there any more left?"), or that you've eaten as much as you'd like to ("I'm done with my apple pie; does anyone want the rest?"). It does not necessarily imply that you didn't like it, but if you say this after eating only a little bit, people will likely infer as much.