First of all, you must relinquish the idea that shinobi is some sort of caste. "Shinobi" is actually a very broad term that includes any operative that is acting covertly. This includes anyone that was sent out as an assassin or, more regularly, a spy. In fact, one of the most famous ninja of feudal japan was Hattori Hanzo, who was a samurai general serving under Tokugawa Ieyasu. The majority of shinobi were, in fact, samurai. This is because, at the time, the samurai specialized in warfare above anyone else in Japan. Therefore, the most qualified people to undergo a covert operation would be a samurai.

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When people speak of "ninja clans" or Shinobi as a people, rather than a role, they are referring to the Iga and Koga clans. These clans are the exceptions, where entire villages had traditions of raising people to become Shinobi. Unlike popular portrayal in the West, there was no feud between Samurai and these Ninja clans. In fact, samurai from all over Japan would hire Iga and Koga ninja to enter their clans and serve them as samurai or highly specialized soldiers. The only time Samurai and Ninja fought as opposing factions was with Oda Nobunaga, who saw them as a threat and sought to eradicate them. Even then, it was less "Samurai vs Ninja" but more "Oda vs Iga".

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So, to answer your question, shinobi would be treated the same level as samurai, because they were samurai. Even the Iga and Koga clans would more often than not become samurai once they left their home borders. If not employed as samurai, they would be employed as footsoldiers, who would be on the same level as a farmer (which was still high in Japanese hierarchy). And the ninja who stayed in Iga/Koga were not part of the general hierarchy because they lived in isolated villages of their own.

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Furthermore, to give you a better idea of feudal Japanese hierarchy, the Shogun is also a samurai. Shogun is short for sei-i-taishogun, which is similar to "supreme commander". It is a title given to the samurai whose responsibility was to unite all other samurai during a foreign invasion. Therefore, while he is above all other samurai, he is not separate from the samurai caste itself. The hierarchy was theoretically of the following:

Emperor>Court Nobles>Samurai>Farmer>Artisan>Merchant.

I say theoretically because the Emperor and Court Nobles were often reduced to puppets by the samurai who theoretically 'served' them. Hence the real hierarchy would be

Samurai>Farmer>Artisan>Merchant,

with the Shogun being the top samurai. Merchants were the lowest because they were seen as producing nothing, but rather taking things that other people have produced and then selling them. People such as criminals and burakumin (dishonorable jobs such as cleaning feces) were not considered as part of the hierarchy at all, and instead were part of their own isolated category.