Its easiest on their system to make the switch 1 oz at a time (for example: 3 oz formula, 1 oz milk; a week later 2 oz formula, 2 oz milk...and so on).
With my son, we eliminated the bedtime bottle first, at about 9 1/2 months (we started giving it to him before bath instead of after) and at 10 months we got rid of the bottles and switched him to sippy cups.
Also, whole milk is needed for the first 2 yrs because they need the fat for brain development. I don't spend the extra money for organic milk because if you read all milk cartons (at least here) they tell you that there are no hormones or antibiotics given to their cows.