You know, I was at work thinking about this topic, saying to myself, "How would I explain the differences between ninja and samurai with an analogy?" The best one I could come up with was CIA agents vs soldiers, so in that we agree for sure.
Sure, technically media could be used an example, but the differences between the two in media are GREATLY exaggerated for distinction and artistic flair. People think the whole 80's ninja thing is really cool, the idea that there are these guys who used to dress up in cool ninja gear and infiltrate enemy compounds and assassinate guys in really cool ways and that sort of thing. The thing is, a more accurate representation of shinobi might in fact be a lot LESS exciting, so they buff it. The best definition of "忍" I've seen is "perseverence," as in, to steal a line from Lone Wolf and Cub, "the shinobi endures with dagger in heart, the shinobi endures of the torture of deceit," et cetera. Many of them spent their lives in disguise, living as other people, or doing tasks that most warriors would find repulsive.
To anyone who says that ninjas were NOT greatly skilled fighters; did you know that in warring times before a castle siege, ninja teams used to infiltrate enemy forces disguised as castle defenders, to set fires and launch guerrilla attacks? These tasks involved quite a lot of fighting, and could easily be compared to current-day Special Forces kind of unconventional warfare. In this sense, they would probably be better compared to, say, Green Berets or something. They had training in areas that FAR surpassed samurai military education.