There hasn't been any evidence in any of the reputable sources I've checked to support the illegitimacy of Toyotomi Hideyoshi's son.

I did, however, come across Learning from Shogun - Japanese History and Western Fantasy, which mentions briefly the idea that Hideyori wasn't Hideyoshi's son

Even while alive, [Hideyori's biological mother] suffered many malicious rumors about the parentage of the heir Hideyori, whose elegant good looks were in disconcerting contrast to the simian features of [Hideyoshi]. (The suspected father was not Ishido-as-Ishida, as intimated in Shogun, but rather Ono Harunaga, who led the Osaka forces in 1614-15 and acted as [her] second at her suicide.)

However, the book doesn't seem to expand upon this line of thought much further, so I wouldn't see this as anything to build upon or to serve as evidence. I also found this blog post, however I always have my reserves about blog posts since, well, they are rarely, if ever, valid or reputable. In the post, the author talks about some professor using

the theme of undocumented historical events (events in which no solid proof exists) as a topic for his latest work "Kawara no Mono, Hinin, Hideyoshi" (河原ノ者・非人・秀吉 - vagrants, castaways, and Hideyoshi).

Undocumented historical events is what I took from this - essentially, conjecture and hypothetical fantasy. Again, nothing that can conclude, with minimal doubt, that Hideyori wasn't Hideyoshi's son. However, there are few sources that deal with the legitimacy of heirs of daimyo in pre-modern Japan, given that it isn't really a point of interest for most historians, so it could be possible (though I highly doubt it) that Hideyori isn't Hideyoshi's son.