My opinion is no. A 6 year old shouldn't go to a funeral - especially not for someone he didn't know. It's a somber, often emotional event that's difficult enough for adults to endure. I personally think it's unfair to subject a young child to a funeral unless you are prepared to leave if the child gets upset, bored, etc.
Unfortunately, I don't believe you have a legal say about what your ex-husband does during his visitation period unless there is something in your Parenting Plan that specifically gives you veto power. Is there anything in section 2.1 or 2.2 that restricts his right to make decisions about your son? What about in section 4 - which discusses decision making? If you have any questions, perhaps you could call your divorce lawyer and ask him/her?
I've drafted a number of divorce pleadings and I have never included language that would prevent a parent from attending a funeral with his child. (After reading your post, I may start though.) I've also never seen a Parenting Plan that allowed joint custody that had this kind of restriction, so I'm not too optimistic.
Anyway, do you have a reasonable relationship with your ex? (I know, I know. Silly question, but I had to ask.) Perhaps you could say something like, "I was wondering if you'll be taking our son to the funeral. I'm a little concerned that it would be hard for him to sit quietly and be surrounded by people who might be sad, emotional. Do you think there are some books or toys I could send with him that he could take to the funeral to keep himself busy and entertained?"