Yes, there are a few people here specializing in the history of Japan. But what exactly do you want to know? The way you phrased this, it sounds like you want an entire book briefing you on about a thousand years of history, which is a tiny bit too vague :)

But maybe browsing our FAQ on Japan, especially on the following topics, can give you a first orientation:

Samurai

Warfare (also with a subsection on ninja)

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Also, if you're really interested in "all of it," I'd suggest getting a book or two.

For example, Nancy Stalker's Japan: History and Culture from Classical to Cool is, despite the title, a good textbook-level introduction on Japanese history in general, and Michael Wert's Samurai: A Concise History probably the best concise (duh!) history out there. Lopez-Vera's History of the Samurai is more in-depth, but its first few chapters are not the best treatment you can find on early medieval samurai (its fine for past the 14th century though). There's more books out there, but I'd need to read those first ;D

Check out the ninja section on our FAQs.

As for whether or not ninjas were samurais, the answer would be...some were and some weren't. There are quite a few points to consider.

Shinobi/ninjas were impercise terms, and in fact not standardized either. In fact they were generally called by the name of their group, usually where they came from. "Shinobi" was more often than not used as part of a verb, to "sneak"ly do something. In the sengoku such duties would likely have been hired out to locals. Many of the time these were given to low-ranking soldiers, local hunters, or even bandits. A lot of samurai, at least high-ranking samurai, would've likely considered these duty unbecoming of their stature/below their paygrade. However a lot of samurai were turncoat spies, bribed or negotated to give information or switch sides. Also there's nothing really stopping the task from being assigned to low ranking samurai. The class divide was very unclear at the time anyway. Once in the Edo period, as the divide between those who were warriors and those who were not was increasingly made clear, any men still employed to do scouting/spying (or really, to do anything) were probably warriors, or at least warrior-servants. We know of a group from Ōmi province that was brought half way accross Japan to infiltrate the rebel castle during the Shimabara Rebellion. They were probably warriors or at least warrior-servants. They failed by the way.

Both when people think ninjas were not samurais but commoners who overthrew samurai and when people think ninjas were samurai, they're usually thinking of the so-called Iga ninajas, and to a lesser extent similar group in nearby Kōka. While the group was the most famous in popular culture, their actual history is very murky. The people of Iga predominantly live in its isolated mountain vallies. Early in the sengoku the people of Iga killed their lord, and from then on they ruled (and fought among) themselves. Until Nobunaga came along, no one was able to assert control over Iga. The Iga people were able to use their knowledge of local area to ambush and defeat anyone who tried, including Nobunaga's men, but eventually succombed to Nobunaga's overhwleming forces. It's important to note that we should not think of these people as starving, down-trodden farmers who turned farming instruments and everyday skills into ninjutsu to overcome oppressive lords. While sources are scarce, it would appear after ousting the lords, Iga was ran by about a dozen families. Given the power they held, they should be considered jizamurai and likely were already local leaders before they ousted the lord. And they happily hired themselves out or allied themselves with outside lords if it served their purposes.

After Nobunaga was assassinated, Tokugawa Ieyasu travelled through the area trying to escape back to Mikawa. His vassals Ii Naomasa and Hattori Masanari were able to hire a couple hundred locals to escort them for the rest of the way. Afterwards, the Tokugawa hired them. Because the Hattori was originally from Iga, Masanari (popularly known as Hanzō, and he wasn't himself born in Iga) was given charge of the Iga group. After the Edo Bakufu was founded, the Iga group was one of the samurai that guarded Edo Castle. They were officially listed as gunners by the way.

But you can see how all these internet labels came from the story of the people of Iga. None of the labels are completely wrong, but also none are very accurate.