My TOS set should arrive at some point today and I'm looking forward to watching the show in 1080p with 7.1 surround sound!
I believe the blu-rays are in air date order but I recommend you watch the start of the first season in production order starting with the "Where No Man Has Gone Before". You could also watch the original unaired pilot "The Cage" first which I believe is included with season 3. Most of it gets shown later in the 2 part episode "The Menagerie" though so it's up to you.
You can find the episodes in production order here.