This is probably the closest comparison I have seen so I see why this is a tough decision.
First I would say go with your gut. If you felt on interview day that you liked the people at Stony Brook or UConn more then go with that.
Price is going to be pretty consistent at either school.
UConn has TBL which can be a pro/con for some people. I personally think TBL teaches a valuable lesson in how to become an independent learner. Plus TBL is only for BMS which is three days a week for just over 1 year (in the grand scheme of things it's not that much time)
I saw people talking about match rate. This year UConn for Phase 1 has 1/1 endo, 6/6 pros and 5/5 ortho. Phase II happens in Jan so we will know more then. Each year we have had virtually 100% match rate in all specialties and gpr/aegd but I am sure Stony brook is similar.
I think class sizes are pretty similar as well. Uconn is just about 50 students.
UConn is 100% p/f which is absolutely amazing. I saw someone say it puts more emphasis on things like the CBSE or ADAT which is true but at the same time we do extremely well on those tests so it takes a lot of stress out of the day-to-day dental school.
UConn has brand new clinics - don't know if that should be a deciding factor tho but its a bonus.
One difference based on talking to Stony brook students is they have much more requirements then UConn in terms of clinic. This again is going to be a pro/con for different people. One way of looking at it is you get to do more and potentially become better/faster at whatever the procedure is. My take on it is I do what I need to do to feel comfortable and confident with each procedure without having to do so many that I am just stressed out (not saying that SB requirements are overwhelming I have no idea). Doing more of something does not always correlate with being better. Your opinion on this will probably change based on your goals in general.
Do you plan on doing GP or have a specific specialty in mind? I think that will help me provide you with more info.
Either way, both great schools, very similar programs