I'm sure you got your answer by now but in any case here it is, for future reference:
- You get Honey from the Village Shoppe, as well as apples, citrus fruits and all other stuff.
- If you are questing with the Physician (and have Pirates and Nobles EP), remember to STOCK WITH A LOT OF HONEY and Apples and Citrus Fruits. You can only get a small amount a day and it's much needed for your tasks and quests. So I suggest buying them everyday. I wish I had done that!
- In case you were wondering, it's the only place where you can buy it.