It's NCIS but I figured I'd do it for NCIS Los Angeles as well.
I think it would have to be season 2.
The first season of any show is always a case of TPTB feeling their way with regard to a show and IMO, it wasn't until S2 that they really hit their stride. Adding McGee as a regular (and Palmer as a recurring role) really added to the season.
(2nd favourite would be season 6 when they brought in Vance as a Director who wouldn't take any crap from Gibbs)
NCIS Los Angeles
Easy answer, definitely Season 2.
And yes, I will freely admit that the addition of Deeks to the team added an element which I hadn't noticed missing from S1, but which I now miss when I rewatch older episodes.
Season 4, without a doubt.
We had to watch a whole season of Tony doing his undercover operation...sorry, 'dating a new girlfriend', only to have this 'shock revelation' in the finale that this was part of a mission. Only problem was, many of the audience had figured out half a season earlier that Tony *had* to be undercover with Jeanne, as he would never have blown off his job for a date.
Knowing now that this was all part of Jenny's personal vendetta makes it even harder to stomach watching that season. Add to that the shoddy way Tony was treated by the team when they found out and the beginning of dumbing down his character, and blech, just blech.
Season 5 would be runner up, as we had to watch Tony being treated like crap by his teammates, just for doing his job. Plus Jenny seemed to get more and more shrill and crazy as the season went on, until finally it was a relief to have her killed off.
NCIS Los Angeles
well there have been only 2 so far, so it's not so much 'least favourite' as simply 'less' favourite. So I'll go with season 1, simply because it doesn't have Deeks!