Season One definitely. Most of the reasons I feel this way have already been posted. It was just a better show in season 1. I loved the grittiness to it and the "realness" of it. It has veered so far towards being flashy and glamorous that it barely feels like the same show. I also like the characters' interactions much better back then. And I think the addition of a poorly developed and poorly acted character in season 2 as a replacement for a complex, well-acted character was an enormous mis-step.
Season 1. The rest are a jumble, but probably S3 taken as a whole would follow, with the others only palatable for specific eps within them and not each for their entirety. Agree with most of the reasons supporting S1 that others have said. Loved the tone, cohesiveness, grittiness, to the stories and the characters, the cast dynamics were solid, the fact that there wasn't catering in the form of stunt casting and so many uber tech toys and production slickness, and the cases were interesting. They've been mucking about trying to fix a lotta something that didn't seem quite so broken in hindsight.
Season 2 is my fave. i started to really get into the show and really get into the characters in this season. i had a good time watching Lindsay as the new person and all the characters were beginning to grow. i really go based how i liked the episodes and the eps in this season i can watch over and over and never get sick of them. Season 1 was amazing it really captured what makes NY so diverse and the characters were played as true hard ass NYers. they were people i can picture seeing on the streets of NY just walking around or fighting crime. Aiden to me was the epitome of a tough ass NY chick to me she was so real and so appealing. Danny was perfect the way he was written just attracted me to the character. now i just look at NY as being a different show completely from season 1 and in a lot of ways it does suck that it changed so much. maybe i'm just saying this as an Aiden fan but i think the show lost a lot of its edge when she left. i wonder what the show would have been like if Vanessa Ferlito had stayed, maybe it would still be edgier, like i said she was the realistic tough NY chick and that's missing. the biggest thing from NY that is missing is the diversity from season 1. i am sick from past few years of seeing rich people with problems there aren't cases where we can relate to the people. Season 1 of NY is the best S1 of any show i have seen. the writers did a fantastic job of making it differen and realistic.