I know someone whi is in prision and is a non-custodial parent. He wants to see his son who is 5 years old and the son wants to see his father as well. The ex will not allow them to see each other and also any of his family, I am just curious on what can be done so they can see each other.

He needs to go to family court and apply for visitations.
He may only be granted supervised visits but it would be a start.

Thjis depends on whether there is any previous court ordered visitation. Either way, he has to go to court to enforce an existing order or ask for the establishment of a new one.

Does the fact that he is in prison have any bearing? I'm not sure I'd want to be taking a 5-year-old to prison to talk to daddy, myself.

A judge may certainly uphold the mother on not allowing visits while he's still in jail.