A.C.
One thing that has helped my children's relationship with their dad is to have good stretches of time with their father when I am not around. They do fun things. They work together. They have their own relationships that are completely unrelated to their relationships with me.
This can be especially challenging to us homeschooling moms, since we tend to be so central to the lives of our entire families. All the same, your children are old enough. You could join a book club, knitting circle, scrap booking group, take a class, or start having breakfast with other mom friends on Saturday mornings. If that doesn't suit you, then what about encouraging father and son to spend time sharing a hobby they both could enjoy on a regular basis?
Good luck! Perhaps this phase will lead to a better relationship between the two of them in the long term.