You may have to start the process over a few times if he becomes fully aroused after being put into the crib, but eventually you will learn when the time is just right for moving him from your arms to the mattress. Once your infant can put himself to sleep you will need to begin to wean away the various incentives that stand between you and a good night's sleep. Likewise, offering water or a pacifier in the middle of the night only teaches your baby to rely on you for those things, resulting in the same need for attention that feeding causes. You are best leaving a half dozen in the crib before you go to sleep so that he can soothe himself without you. As for water, if you think the baby might be thirsty you should make sure the bedroom is well humidified.
Any healthy baby can wait until morning to drink again.
Of course, if your baby is ill all bets are off and forget sleep training until he is well. You need to be prepared for this and tell yourself that you are a good parent, not a neglectful one, and learning to sleep through the night is a skill that will benefit your son forever. You too are in need of rest and will be a better parent for it. I suggest that you wait a few minutes when your son first awakens and then if crying persists, go to the crib and gently touch his body to both assure him of your presence and to determine if he has a fever. All of this can wait until the morning and the pacifier can be found by your baby without your help if he wants it badly enough.