I'm gonna list mine in the order they aired, because picking an absolute favorite it too tough.
Three Generations Are Enough - A great example of CSI:NY's theme, "everything's connected". Plus I really liked Jane, the DNA lady
The Fall - great character moments for Flack, Eddie Cahill knocked it out of the park.
Fare Game - the watergun game was fun, and the story of the killer was moving
Silent Night - I'm a big Marlee Matlin fan. And her character's comments about how Mac speaks with his eyes were dead-on, Gary Sinise says more with a look than most actors say with a page of dialogue. Plus it was great to see Mac & Peyton get back together
Snow Day - possibly their strongest season finale. Stella & Hawkes as action heroes was pushing it a bit, but Gary Sinise really sold Mac as a Marine(no such thing as ex-) who could still throw down.
Down The Rabbit Hole - really neat case, one of the few where their killer gets away, loved that Adam got a chance to really shine. I didn't think the follow-up was as good.
Turbulence - it was fun watching Mac improvise while on the plane, and I'm glad the passengers who were obvious suspects turned out not to be the killer.
She's Not There - LOVED this episode. Probably the best "human trafficking" episode of the CSI franchise, mostly because if felt the most personal. It wasn't about the brave heroes rescuing a shipping container full of damsels in distress, it was about very specific fathers and daughters. That scene where the one girl says good-bye to her father in the morgue gets to me every time. And Julia Ormond did a great job, I wish they'd been able to have her around more. She & Gary were great together.
Hammer Down - The strongest installment of that CSI trilogy. Lots of people talk about how good Mac & Horatio are together, but I though Mac & Ray were fantastic.
Pot Of Gold - Purely for the introduction of Aubrey Hunter. Madchen Amick was ridiculously charming, and I though she & Gary had great chemistry. I really wish they hadn't dumped that storyline.
Damned If You Do - Interesting story, with some nice character beats for Mac, and one of the funniest bits of the show's whole run, with Jo setting up that fake polygraph test.
Hide Sight - The overall story was ok, but I like this one mostly for Mac's interaction with the girl who lived across the way from the suspect. That scene with them sitting in the windows was lovely.
Party Down - I liked this one mostly because it was just a fun mystery to unravel.
The Untouchable - Very touching story, Gary always does such a great job when Mac's connecting with someone like he did with the victim(I think I'm one of the few who enjoyed his scenes with Ella McBride a few years ago).
Exit Strategy - An excellent episode that had some great moments for Mac & Jo's friendship, and a great story for Mac overall. They were in a tough spot creating an episode that could provide enough closure if it was a series finale, but could also lead them into a new season if they got picked up.
As you can see, the season with the most entries on my list was Season 7. I know Stella has a lot of fans, and I never had anything against her, but she wasn't all that compelling to me. By Season 6 I thought the show was getting a little stale. Sela Ward as Jo Danville was a breath of fresh air last year. Her addition to the team, and the shift in focus to mostly single-case episodes which allowed for richer storytelling really gave the show the boost it needed. I can't wait to see what they do for Season 8.