There's a few things I'll mention that have helped for us. But first, a tiny bit of background:
Our 'problem' initially was Jitzu refusing to accept Torri. Now, with Jitzu being older and not particularly healthy she simply doesn't have the energy to be a jerk to Torri. (Not something I'm completely happy about, since it took chronic illness...but I'll take the silver lining on this particular cloud.)
Unfortunately, Jitzu's bullying led to Torri becoming very shy, reserved, and anxious. this makes her a target or the boys.
She's 6 years old now, and things have improved significantly in the past 3 years. I still don't think she'll ever 'like' the other cats, but they're getting much closer and there are days when she'll even play with the boys! (and there play is getting longer and less combative
Mainly, we gave Torri her own safe space and kept her there to build her confidence. For about 6 months solid she was only in one room (ours) with everything she needed. IMO this isn't cruel, because the option was re homing an extremely anxious cat...That works best in some situations, but not for us. After 6 months she'd had a huge change in personality with myself and my bf; she was sweet, snuggley, playful, and much happier.
As time progressed and we began letting her out while we were home we worked on her confidence out of the room. Having 'family treat time' every night was a HUGE help. Torri sat on the table and got her treats there, the other cats got theirs on the floor. Now, Torri will sit right next to any of the other cats to get her treats, but it took 6 months or so to have her feel confident enough not to run away and hide. (I do an alternating pattern, each kitty gets one treat, then we start over and eah kitty gets another treat, ect. So they need to wait their turn.)
Making sure the boys get enough exercise is another big part of things. If they're full of energy and mischief they just can't help but tease her, if they've just have a big run then they're over all calmer and better able to have good manners.
So, basically, I'd try two things. It doesn't sound to me like you need to separate your boys, but I WOULD do daily play times, focusing on the older guy. Also, try doing treat sessions twice a day or so, you don't need to give them tons of treats every time, and it doesn't need to be 'cat treats' from a baggie either! I use tiny bites of cheese, chicken, beef, chicken pure bites, and cat kibble mainly. But I've used a zillion different things in the past year, lol. The only thing that matters is that they like it! Since they're only getting 3-4 bites it doesn't really matter what it is, as long as it's not always lunch meat or tuna, lol.
Giving your older boy attention is a good idea too...but I'm more of a fan of 'who ever is behaving best gets attention' than 'you were here first so I love you more' brands of cuddling. If you've had both boys for 2 years it's not like you're less attached to the younger one, and coming second doesn't make him a lesser citizen! (certainly not at this point anyways!)
I give all my cats equal amounts of attention, in different ways and when they're behaving. (Ie don't' give the cat who's scratching up your couch a snuggle right that moment).
I see it like having kids. Do you pay more attention to the first one once you've got a second? Nope. Not fair.
You also need to be careful how often you yell at the older guy for chasing the young kitty. If he's always getting yelled at when the younger cat is around it can actually make things worse! "I always get yelled at when that darn younger cat is around. I HATE that guy!" Cats don't always link their actions with consequences. Make a point of talking nicely to the older boy, and using your voice to (positively) distract him from stalking the younger one.
The more positive things you can connect between the two cats the smoother their relationship will become. " When that young guy is around Mum seems really happy and I get loads of treats and cuddles! I like that guy!"