Congratulations! These are two fantastic schools, and you really can’t lose at either one of them. My prospective CS-major son faced the same decision last year, and it was incredibly hard (on us too, since we’d all fallen in love with Yale). He finally chose Stanford, primarily because of its reputation in that field, and though he’s not planning to major in CS anymore, he doesn’t regret his choice.
I’m assuming you’ll attend Admit Weekend and Bulldog Days. You especially should visit Stanford to get more of a feel for how you’d like living in California. It’s not sunny 24/7, but it’s definitely sunnier than New England.
In addition to visiting, though, I’d encourage you not to focus too much on particular departments’ reputations—unless there’s a problem with the one you’re interested in. That’s definitely something you should consider then, and if you feel Yale isn’t particularly strong in biology and Stanford is, that’s an important factor.
On the other hand, keep in mind that 50% (or more—I just saw an even higher figure recently) of entering freshmen ultimately change their minds about their major. We didn’t expect our son to be part of that 50%, but he turned out to be. So it might help to think about several possible majors you could end up choosing and see how Yale’s and Stanford’s programs in them compare. Maybe they’ll be comparable, or maybe one school will be better in one field but worse in another. What’s important is that you have good options in anything you might be likely to choose. (Luckily for us, my son’s two other most likely majors now are top-notch at Stanford; one of them would have been quite a bit less strong at Yale.)
Beyond that, though, think about what you want the totality of your college experience to be like. It sounds like you’ve already given that some thought, which is good. Some people feel that college is a time to experience as many new things as possible; if that’s true for you, then choosing Stanford might make more sense. But no matter where you go geographically, you’ll have endless new experiences, so if you love New England, there’s no need to force yourself to live somewhere completely different, especially if you don’t think you’ll like it.
I can’t really speak to the strength of each school’s pre-med programs and placement, though I’m guessing both are great.
Financial aid, though, is usually important for many people, and if you end up getting significantly more aid from Stanford and money is a factor for your family, that’s definitely something to consider. A free ride is a hard thing to turn down, especially if you’re comparing that to having to fork out a lot more money over four years.
Good luck with your decision—Stanford and Yale are both wonderful places, and I’m guessing you’ll have a terrific college experience no matter which you end up choosing!
It sounds like he is currently enrolled at S after initially enrolling at Y but he is having doubts again.