First off is your girl altered?
Second since she is only showing aggression towards your one child are you sure he's not maybe being a little ruff with her? Often times young children don't understand when they are being too ruff &/or actually being mean to an animal.
So many parents say "Oh no he/she would never do that, or No, he's so good to fluffy, & loves her so much" only to find out that the child actually is being not so nice to the pet, & is maybe just doing it when there is no one else around.
Something about the whole situation just doesn't mesh, It would make more sense if your youngest came into the picture after the dog, but based on their ages that's obviously not the case. Dogs are not vendictive (sorry not sure how to spell that one this early..LOL) creatures. They don't just wake up one morning & decide not to like someone for no reason.
The first thing I would do if Jenna is intact is have her altered, then you need to be sure that your little one isn't maybe being too ruff at times, then I make an appointment with my vet to rule out any possible health issues/illness in Jenna. (Often times when a pet suddenly starts showing aggression &/or behavior problems there is an underlying illness, infection etc).
If there is still a problem after all of these things are done, I would consult a trainer &/or behaviorist to see if they can offer a solution. I seriously doubt that it's an issue specifically with children, especially since she does well with your six year old, & she was raised around children. Plus the breed as a whole is usually naturally good with children.. It's part of what Boxer's are known for.
I totally understand your concern for your sons safety, but often times situations like this can be easily fixed, with no future problems. Sadly though because it is so scarey people often jump the gun & immediatly give up a beloved family pet, without trying to find the source of the problem.
Good Luck!!! Hope this helps.