I’ll be contrarian here and say that we have flown in and out of LaGuardia several times in the past year, multiple family members on several different trips, with no issue. The reno of the terminal looks great!
With only three days, I would stay in NYC. That’s a short trip to be planning visiting schools at any distance.
I’ve driven to Philly in an hour and a half starting north of the city, so it’s doable as part of a three day trip. OTOH there’s a lot to do and see in NYC and the surrounding area. Lots of colleges in the suburbs as well as the outer boroughs. I second taking a look at Fordham if you’ve got a kid who really wants to be in the city.
As another poster said, an hour and half on the train and the trains seem to leave every half hour on a weekday morning. Carnegie Mellon is not. It’s a six to seven hour drive and much longer on the train.
Agree with others who said that 3 days in NYC is not very long - probably don’t want to dilute the experience by even going down to Philadelphia which will take the better part of a day if you consider 3 hours plus RT on Amtrak , time getting to and from campus (though Penn and Drexel are very close to 30th Street station in Philadelphia), time to tour and look around etc.
Even though you’re visiting niece at NYU, may need to expand your hotel search slightly to get a reasonable room for $250/night. If that’s your “all in” price, be aware that NYC hotel tax is very high and many hotels now charge a daily “amenity” fee . April is also the start of prime tourist season. There are some reasonably priced Hiltons and Marriotts in midtown east that would be an easy subway ride to NYU.
Agree with EWR for quick public transit in and out of the city.
Many different colleges have been mentioned and all levels of selectivity. If you’re trying to convince your D to like east coast schools be aware that some students find the Columbia tour dry, boring and intimidating.