Sounds like you have 3 problems. Chocolate milk, bottle and sippy use.
If you can't do cold turkey, I'd gradually reduce the amount of chocolate flavor in the sippy cup until there is no longer chocolate in it at all. Then, slowly move to a cup instead of the sippy. Give it to him at meals and tell him there are no sippy cups at the table anymore...only big kid cups, and give him a regular cup. If he's thirsty enough during dinner, he'll drink from the cup. (I'd even add a little salt to his meal to make him a little thirstier than normal for the first few times he uses the cup...then, he'll be sure to get a positive responce from drinking from a big cup, plus...he'll be so thirsty that he'll get enjoyment from drinking from the cup over the sippy. (Salt is generally not used with children much and many moms would probably frown on this action, but I'd do it to curb his appeal for a sippy cup because in my opinion, he needs instant gratification and a positive thought towards the cup. Right now, he thinks cups are bad and sippy's are good. But, if he's thirsty enough, the cup will be his salvation...and yours.)
I forgot to mention the idea of the bottle. Once you move him off the sippy at meals, only offer him the sippy when he would normally get a bottle and tell him, no more bottles, and he'll probably be ok with it once you wean him off the chocolate milk in the sippy. Then, he can have milk in the sippy in replacement of the bottle. Eventually, you wean him off of that. The process could take a few weeks, but be patient and persistant. If your firm, you could have him bottle free and sippy free in a month.
Good luck.