We've been going through a little of this with our daughter. Now that she's old enough I sat her down one night and explained to her that she's a big girl now...and in a big girl bed...and bottles are for babies....Babies need to drink milk at night, but not big girls. We went through all of that and she told me...she still wants to be a baby, and I told her she will always be MY baby, but she's a big girl now.
We pretty much went cold turkey after that. Yet it wasn't too hard for us...because we stopped the middle of the night bottle around a year old for her. (she's now two years old and three months) anyway, she was only getting a bottle at nap and a bottle at bedtime..so we kind of gradually changed nap to a sippy....blah blah blah
Since it's really not about the "bottle" and more about her teeth and what the milk does to her teeth all night...we told her she could have her milk right before bed, in a sippy with a snack. We then go up and brush teeth and do our normal bedtime routine. I told her if she wants to pretend she's a baby she can have a bottle with water.
I think you may need to do this in a few steps...first....get rid of the middle of the night bottle. And sadly you'll just have to let him Cry it out. Maybe move the other one (who sleeps through the night) out of the room while he's screaming and complaining. IT might take a few nights of this before he gets the point. He can have a drink of water at night if he's thirsty...but not milk. Once our dauther realized I wasn't going to give in and give her milk..she finally stopped...but it was a long LONG few nights.
I think after that battle is over...THEN you need to battle the bedtime and naptime bottle. Maybe your doing too much at once for the little guy. He sounds like he's sensative and relys on that for comfort. Yet try to make use of explainging WHY you are doing these things...not because your mean mommy..but because mommy doesn't drink milk in the middle of the night and it's bad for his teeth...Ive found my battles a lessen when I explain things to her...she understands a lot more than I realize sometimes.
I feel for you though...I think I cried with her when then nighttime bottle went away.
Sorry...that was a long one :)Hang in there..but stay strong.