BERG Racing in Webster is worth a look, they are primarily a racing and performance shop, but they also provide service and are VERY familiar with German automobiles.
BERG Racing, LLC
I also recommend Metric Motors, as you can tell from the name they also specialize in import service.
Metric Motors | Rochester, NY Full Service Auto Repair and Sales
As well as CDI Auto, this place is very well known for their Euro experience, and just to set the tone for their expertise, they are a go-to shop for Ferrari owners in the area who don't want to transport their car to out of state Ferrari dealers.
http://www.cdicars.com/
Last but certainly not least is Eksten Autoworks in Greece. They are similar to BERG in that they do both racing and service work. They've been around forever and have a very high reputation in the area for their Euro work
Eksten Autoworks Import Auto Repair Service and Race Car Preparation. Porsche, BMW Specialists.
You really can't go wrong with any of these shops and it might just come down to whoever is closer to you