Also is there enough stimulation at the places he goes to sometimes they do nap for a long time and boredom will make him very unhappy .. check out the games and fun, maybe reading that they do .As he hasnt seen you both all day do you play with him in the evening?.
Another thought...is there a new teacher or care giver there? I only ask this because my son (much much younger) was in hysterics at his daycare. When I came to get him he would quite literally throw himself at me, not even allowing me to put him down to put his coat on. He was terrifiied, and the situation did not improve. This is normally a very social and outgoing toddler. There were a few other red flags as well. I finally switched him, and the situation is 100 times better. He is happy and actively involved in the activities, once again highly social and loves being there. I don't think there was necessarily abuse involved, but wonder if one or more of the caregivers were less then patient with him, or perhaps yelled regularly or something of that nature. I know your son is older and better able to communicate, but if this change in behavior is new, I might look at changes in the aftercare program. Just a thought.
It sounds like a long day for him away from you, is there any way you or his Dad can adjust your schedule I think the crying shows he is anxious and needs to be with you guys more. Is the schedule till 5pm every day ...from what time 8-9am ?
First, I would make sure that there is no one picking on him in aftercare and that there is no reason why there would be this new distress. If you find out that there is nothing like a bully, you may want to look in to how the children are engaged in the program. While it is normal for some children to be upset about having to stay, they can often be distracted from it. Are they doing homework much of the time? If so, it may be more related to frustration with school work. If there is play time, are they given enough variety? Some kids just aren't engaged by the same 5 puzzles being thrown in front of them everyday. You may also want to inquire about whether or not any of his friends or classmates are in his group (and if not, would it be possible to move him to a group where there is).
If you feel none of the above is applicable and it is because your son is sensitive, there are a few things you can do. First of all, you can get him a digital watch and tell him that he can check the time. Write him a note to keep in his pocket to remind him that you will be back before the clock says 5. Or you could give him a special notebook or journal and tell him that if he feels sad or misses you, he can draw pictures for you or to show you when he gets home. When he starts asking you on the way to school, keep calm and don't show frustration. Instead of answering, turn the question around and have him tell you when you come. Keep it very matter of fact.