Sometimes it takes more than one round of antibiotics, and/or different antibiotics, to knock out an ear infection. But even if that's what's going on, once the infection's cleared, he may still be in a pattern of this kind of waking. I know it's not what you want to hear but...you'll have to tough it out until his body gets past the pattern, which you can help him do by not removing him from the crib when he wakes and giving him only a sip of water --not milk (awful for his teeth in the night).
Also, he may be having a growth spurt as others said; try giving him a regular, high -protein snack every night before bed because protein at bedtime helps kids (and adults) feel fuller and "last through the night" without as much waking. Try a boiled egg, or peanut butter on crackers, or whatever high protein works for him. And do it last thing before bed BUT do brush those teeth afterward. This may help with the waking because he won't be hungry in the night. What he thinks is "thirsty" may be hunger instead; milk is as much a food as a drink, so that sates his hunger.
Do get the ears checked again as well, and try the high-protein bedtime snacks. But I would definitely not let him get out of bed unless he is distressed as if he's had a bad dream. I am NOT a "cry it out" fan at all, but at his age, if he's up because he's gotten into a cycle of waking for a drink and to check you'll come -- do come, but don't take him out of the crib. For a time you may have to stay in the room and maybe sit next to the crib with a hand on him so he knows you're there, but don't take him out or talk to him at all beyond an initial "I'm here" or "It's OK." I found that that technique reassured my daughter that I was there and would reliably come to her, but also that she was supposed to be in the crib when it was nighttime. The periods that I had to spend in her room in the night did grow shorter and shorter and then stopped both because her sleep pattern changed and because she felt reassured. It's not fun for the parent but it WILL pass.