Tomatoes are considered doubtful, if not actually poisonous, although they have already appeared in some southern European cooking. Chocolate has not yet come in, except for medicinal purposes. Just to be fair, vanilla isn't a period flavoring either. Almond milk, ground almonds steeped in honey and water or wine, then strained, is used as flavoring and thickener. Coffee and tea are period in the strictest sense, but not in use in Europe, except medicinally, and even then are very, very rare.
Sugar is available, but is rather more expensive than honey, since it has to be imported.
The next grade is Barbary or Canary sugar. The common, coarse sugar is brown and rather gluey, good for syrups and seasoning meat.