To answer your question, there probably isn't any preference whether the PPI is done by a dealer or an indy, but if indy be sure that they know water cooled Porsche's. Many well known Porsche shops are old time air cooled 911 experts but don't have much experience with the newer water cooled engines.
You'll have to decide what you want, so drive a lot of cars so you understand the differences. Miles don't necessarily mean more maintenance if the car has been properly maintained and even a car that needs a little work can be a great deal - if you're into that kind of thing.
The last thing that I'll suggest is your budget would also allow you to purchase a reasonably nice 996-era 911. I'd highly suggest driving these also as you may find that a 911 will fit your life and driving expectations better than a Boxster or Cayman.
996's are very affordable right now, I bought my 996 for $10K (
http://986forum.com/forums/general-discussions/44227-986-wrecked-got-996-today.html)