From someone who did the LGA-BOS shuttle 1-2x/week for day trips for 6+ months I wouldn't recommend a 5x/week commute for months/years on end
1) my travel was outbound from LGA which meant not having to be stuck in NYC traffic coming into the city which makes the most painful part of her trip the LGA-city part
2) shuttle on a good day is amazingly quick, definitely with a CLEAR + Pre-check combo I caught flights from curb side at T-15 to making the flight at T-5, though repeated exposure to that experience is probably not good for your life expectancy given the somewhat unnecessary stress
3) 2/3 flights out of LGA are delayed so her evening commute will at least every other day be a hustle to get SDC/SDS on the flight that actually leaves early, or indeed getting home at 2am, or staying in a hotel when you don't expect it
4) more than once I ended up having to uber back from Boston to the city since all flights got cancelled (and the last train had left) and I ended up home well into the night (it's fun to fly without carryon until you have no fresh clothes nor toothbrush with you)
5) "the last shuttle" means getting home pretty late every day... to then take the 6 or 7am shuttle back? That sounds not even realistic. My example was 8am shuttle outbound and anywhere between 4pm-7pm back
If the job is that good and relocating is not an option I'd recommend her to plan for a hybrid solution e.g., flying in and out on a quiet / good weather day, and staying overnight 1-3 nights a week as needed. And ask to work some days remotely from home (e.g., Fridays).