Species in a very separate context isn't really the right way to look at it. When you see species, what you're actually reading is 'how genetically similar/different', so to speak.
Tigers and lions can reproduce, but tigers and jaguars cannot. Why? Mostly due to a phenomenon called allopatric speciation. Geographical separation effects on each animal causing differences that we associate with being separate species from each other. In this example tigers and lions have less of a geographical boundary between them, therefore they are closer together on the phylogenic tree in terms of 'splitting off from a common ancestor'.
(Insert much about how genetics work, ie, pleiotropy etc effecting on the genes for 'breeding capability with so and so/parent species')
Bonobos and chimps are one of the two occupants of the 'Pan' genus (the other being chimps themselves), meaning they have a close relationship, more than likely brought about by some degree of separation that has happened fairly recently in evolutionary terms. I'm not sure on their geographical range so i couldn't speculate on that one.
So basically, they're genetically different enough not to be considered chimpanzees, but still share enough of the base genetics to be able to breed. Par of the definition of a 'species' is technically, as Carzeebear said, animals that can produce fertile young, although i can't find any evidence that they do, and the offspring would be neither one nor the other. Think, horse and donkey equaling a mule. They might look similar but their genetics does not marry up enough that the resulting offspring is fertile, or resembles either parent particularly. You'd get less of this last issue with bonobos and chimps but the principle is still the same. If the young cannot reproduce the 'species' would cease to exist.
TL;DR - Yes, they are separate species.
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