I don't think anyone is unaware of his partisanship. But partisanship is only relevant if it affects reporting, which by your statement would seem like we are of opposite convictions. I believe both the old Daily Show (and likely the new one as well, but I never watch it) and Last Week Tonight work really hard to put everything they report/joke about in a relevant context without leaving anything out, and I have yet to see anything hinting otherwise.
I've seen a lot of critique for Clinton on Last Week Tonight, but even if I hadn't, why would that in any way affect their Trump coverage (if still factual)?
But speaking of politifact [1] [2]:
Is it somehow disingenuous to report on Trumps blatant lies? I find it wholly unsurprising that all politicians lie more than "regular people", but I find it supremely horrifying the amount of Trumps lies that are swallowed whole to the extent that Hillary is the one portrayed as "crooked" when comparing these statistics.
[1] http://www.politifact.com/personalities/hillary-clinton/
[2] http://www.politifact.com/personalities/donald-trump/