I honestly can't think of a way 'funny' might mean dishonest or unfriendly. It can mean 'strange' if intended that way. Can you you provide references to the dictionary definitions you saw?
In any case, people will interpret ambiguous words in the way you intend them if you use the appropriate non-verbal cues, such as tone of voice and facial expression. I can't really teach you those in writing so I'd suggest observing people to find out how to do it. If you want to convey a positive meaning, smiling or chuckling when you say it is a good start. If you want to be sure they understand, then add an explanation.
My daughter's teacher is funny. She told a great joke during our conference. (humorous)
My daughter's teacher is funny. She said something really strange during our conference. (strange)
You'll probably have to ask your daughter what she meant when she said the teacher was 'funny', if it's not clear. There's no way of knowing otherwise.
I would advise you not to call someone cheeky, unless you're on very good terms with them and you're speaking casually to them or their friends. It could easily be taken the wrong way. Even if being cheeky is funny, it's still slightly rude or disrespectful, which make it negative under most circumstances. It's actually not a word that I would expect most kindergartners to know how to use appropriately. I'd suggest investigating where your daughter heard it. The kids at school might be repeating something their parents have said without really knowing what it means. They do that often.
On a totally unrelated subject, native speakers use the plural in the phrase you used,
My daughter says one of her friends is funny
If she were talking about one friend, the appropriate form is
My daughter says her friend is funny.
But she's talking about one of many. Many is plural, so 'friends' is plural.