I think she might have been diagnosed with Alzheimer’s by then?
While it's possible (a lot of the time it's a relatively slow-moving disease), I don't get this assumption people tend to make. TWS is 2014, which places this
at least 15 years before she's in that condition, more likely 16-17-18.
She's 68 in Ant-Man going by the 1921 birth date listed on the Wiki. Even if this is later 90s than early, she's 79
tops , and if the movie indeed has time jumps between early-90s and later, and assuming Peggy'd be seen in that earlier phase, she's only early 70s. It's not young, but look at every government agency in the world - more often than not that's about the age these people in the top agency director jobs are, 60s or early 70s.
No real reason to think Peggy's sickly in the late-90s, even less likely the early-90s. Voluntary retirement's possible of course, but you'd kinda figure personality-wise Peggy's hanging around as long as she's capable of carrying out the job.
Sam's the same age now in the modern-set MCU as the Peggy character's supposed to be in Ant-Man, so like circa Age Of Ultron he's only a few years younger than she'd have been into '93/'94. Redford was 78 in TWS, assuming Pierce the character was his same age, he's still running around as a World Security Council guy and liason with S.H.I.E.L.D.
So yeah, unlikely Peggy's still on the job in '99, but 5-6-7 years before that's a totally different story, no reason she couldn't be. Still don't think she'll be in the movie, but timeline-wise it fits.