I would go with Mendon Villlage Animal Hospital. I do not know how it compares to other vet prices in the Rochester area.
South Rochester NY Area Veterinarian | Mendon Village Animal Hospital, Mendon NY
They are the vets that figured out the aflatoxin stuff with Cornell. They have an eye specialist that comes in as well as a great radiologist that does ultrasounds there on certain days.
I would ask what to do in emergencies. I don't know if you've had a pet before in the Rochester area, but VSR is the main emergency/24 hour vet and I just like to know in advance what I would need to do if there was a problem after hours. I see it on their website but not a lot of detail.
They help Big Dogs Big Hearts Rescue Buffalo NY Rochester NY
dogs when we get a weird case and are really caring and good.
Congrats on your pup!
EtA: Forgot, heard good things about Clark too, and have had animals seen very successfully by one of their newer vets, but no real experience there: http://clarkanimalcare.com/