Congratulations. I think Harvard and Pomona attract very different students, while Pomona and Yale are more comparable to each other. It’s funny because Pomona and Yale have the same school color as each other :p.
It really depends on “fit”. I think Yale is a happy medium between providing the liberal arts and residential experiences of Pomona with the prestige and opportunities of Harvard. Personally, I didn’t pick Yale because I was drawn to the California atmosphere and an exclusive liberal arts experience rather than a liberal arts college within a university sort of deal. But over my four years, I have come to realize what a special place Yale is since I have a bunch of close friends there- so, so many incredible opportunities, and the type of students who go there- they’re incredibly distinguished. I don’t know what I would have done if I was asked to make the decision today. For all the glamour and exceptionalism, Yale is also kind of an intimidating place. The expectations are high and the atmosphere feels decidedly cold for those who’re struggling. Pomona hardly feels like that- it’s humble, nurturing, and for lack of a better word…homey. There was a really nice thread on someone who was deciding between Stanford and Pomona (http://talk.collegeconfidential.com/pomona-college/1764325-pomona-and-stanford-p1.html), and they picked Pomona:
“Lastly, I also picked Pomona because I thought that it would be best for my personal growth. As someone who wasn’t the most confident kid in high school, I felt like a smaller school would allow me to keep myself and my development as a person in check. People know you here, people watch you. I may have made that sounds creepy, but all I am trying to say is that people notice and care for you. You will not be forgotten. And in order to work on my confidence skills (and you may be facing other pero snap issues which could be better tackled with a smaller community), I felt like a place where I would have to speak in classes and be conscious of myself in my environment/surroundings would be best for me.”
I think that’s very accurate to the deeply intimate experience you’ll get at Pomona, but not every kid needs or desires that. There’s another article here about a college president who has one daughter at Pomona and the other at Columbia, though given Yale’s residential system and college masters, it may provide these experiences as well: http://www.huffingtonpost.com/l-jay-lemons/the-gold-standard-the-powerful-impact-of-residential_b_4633443.html
Good luck with some excellent choices, and definitely visit if you can. If your D picks Pomona over Harvard/Yale, she won’t be the first one. Not many do, but there are usually 5-10 kids in each first year class who turn down HYP to go to Pomona.