I am not a New York resident and I had a tough time choosing between these two. I found a few things that you may not know:
1) At New York, every dental graduate will have to do a year of gpr, so Columbia or Stony Brook , you will be experienced enough to practice dentistry.
2) Stony Brook is cheap, but Columbia offers scholarships ( If you deserve it you can get 50K at first and more during the four years)
3) P/F/H or A/B/C system or Nice proffs at Stony Brook or mean at Columbia, they all make you work your butt off
4) Stony Brook has a lower specialization rate just b/c the majority of Stony Brook students happen to like general dentistry, but they are well qualified and will not have a problem getting into residency programs
5) Stony Brook has a limited research opportunities ( 5 for entering class) but Columbia has unlimited spots for research
6) The new curriculum at Columbia is not supposed to "fix" anything, it is because of the new boards exams arrangements. When boards go P/F, there will be another subject test for the specialty you want to apply.
We have nice profs?
All right, for most classes yeah we have nice professors, but we have our fair share egomaniacs who like to treat dental students like crap.
Stony Brook, the town, is aweful. There's nothing to do out here. It's a two hour train ride into Manhattan. The beaches during the summer are pretty much the only saving grace. Honestly, this is the worst aspect of going to school at SB.
If you want to do research out here, there really isn't much competition for the research grants, and there are some quality labs.
As far as academics, I'm pretty sure our stats for our entering class were about the same, if not better than Columbia's. We take basic sciences with med students. Classes are small so professors watch us like hawks in dental classes (for better or worse). Don't feel like you'd be coming to a lesser school by any means, in fact, quite a bit of our faculty have teaching roots at Columbia.
Clinic, we start the beginning of second year with operative and pedo, so there's plenty of prep there. I've already placed a stainless steel crown in pedo as a second year... that's not happening at Columbia.
Don't worry about specializing. I can't imagine specializing because money is an issue for me, and because Stony Brook has kicked my brain's ass. Even the residents here say SB works us WAY harder than their schools ever did. That being said, it's commonplace for our students to get into their first choice for whatever residency they want to do be it GPR or a specialty.
Both schools are great school. For me it came down to cost, and so Stony was the choice. BUT if you can afford Columbia, go there, I miss NYC way more than I thought I would.
You've probably already made your decision, but I'm tired of studying so I figured I'd go off on a little rant.