In my experience positive reinforcement works much better than taking things away. As Tracy K described give him some special time with you when his days go well. Latch onto the smallest bit of improvement to reward.
My granddaughter, who is 11, was having difficulty getting her chores and homework done. My daughter, at the suggestion of their counselor, told her she could do something special when she'd successfully completed chores and homework for a week. My granddaughter chose going on a bike ride with her mother. It is working. Now.....that the rains have started they have to decide on something different. On the plus side, my granddaughter has gotten into a habit of doing those things without always having the bike ride. (no ride when it's raining, mom has a migraine sort of situation)
I also agree with having a talk with your son. Talk with him while expressing concern with him having difficulties. Be sympathetic. Tell him you want his input into solving this problem. Ask him what he thinks should be done. Above all do not lecture or issue ultimatums. Just a quiet collaborative conversation.
Talk with his teacher about what he is doing and why she thinks he's misbehaving. Ask her for suggestions. Consider having the discipline be related to the misbehavior.
Is this the first time you've had 45 minutes to get thru a timeout? If not, timeouts aren't working for him. My grandchildren did not respond to timeouts. They just made them angrier and took the focus away from the lesson to be learned.
Again, at the suggestions of a counselor, my daughter started time in their room for misbehavior at home. They could play but could not come out until they could say they were sorry for what they'd done. When they did come out and offered an at least quasi apology she gave them a hug and restated the rule. Usually they gave a sincere apology after that.
The counselor said that for misbehavior at school, leave the discipline to the school. By the time they come home, the incident should be over with. I suggest that the added consequence when they get home keeps the negative atmosphere going which makes it even harder for the child to focus on being good. The negative thoughts overwhelm the positive wish to do good. Talk to the teacher about this possibility.
I would also talk with the after school care person and find out how he behaves there and what techniques they use that keeps the kids on track. If a child misbehaves (and does yours?) what do they do?
Talk with them, asking for information in a positive manner. If you express the need to also punish at home then they may be reluctant to tell you about the normal misbehavior after school.
Both of my grandchildren's teachers and after school care professionals have told their parents about their concerns for behavior. They have not expected that the child be punished at home. They are only giving the parent information at the beginning. If the behavior becomes a chronic problem they discuss possible ways of handling it with the parent.
Taking away things is just one way to handle it. I suggest it's not effective for most children because they can do without and it's totally unrelated to their behavior. It doesn't teach anything about appropriate behavior. Neither do time outs. Time outs work when the child needs to be separated from misbehavior so that they can get a fresh start. When a timeout happens hours after the misbehavior it just feels like punishment and doesn't teach anything. It does create anger on the part of the child and when he doesn't comply anger for the parents.