This sounds exactly like me before our trip in December. Ella was down to one bottle at night, before bed. (She was turning one during our trip) I took a bottle on the plane anyway because I was hoping she would drink from it during takeoff and landing. Well all she's ever had out of a bottle was milk and she didn't want anything to do with it because I put water in it. It's a double-edge sword, so to speak. Can't take milk because it would be out too long. Can't keep the milk cold so that it's safe to drink because she doesn't like cold milk.
All of our kids were off the bottle at one year old. If he doesn't want it, be glad you don't have to battle him to get it away. My only concern is for his ears on the flight.
Ella adjusted pretty well to the sippy cup, but will only drink milk in it if it has strawberry Quik mixed in. Checked with my doctor and she said that's fine, at least she's getting her milk.
So you could try adding some flavor to his milk. Babies this age only need 16 oz. of dairy and you can count cheese and yogurt, if he likes those.
Crying at night could also be teething or bad dreams, or just separation anxiety. Ella usually sleeps all night, but from time to time she'll cry for no apparent reason. I've had to do the "cry it out" several times. I give her a kiss, tell her no-no, go night-night and leave the room. She still loves me.
But, what do I know? I'm just a bad mom who lets her kids go to the parks when they've been running temperatures. Be careful down there! There are germs everywhere!
Good luck!