There is a third choice: neither. You're in Toronto for crying out loud - despite the kvetching of its residents the TTC is one of the best transit systems on the continent.
Uber is shady as fuck, so is the cab industry. Pointing out the degrees to which they are shady is not particularly useful and serves only to rationalize supporting unethical actors.
There's nothing wrong with roundup-ready corn either (well, any more than what's wrong with regular corn), but I still take issue with Monsanto.
Microsoft still made immensely popular and good products, even while they were stomping all over the tech industry in the 90s.
I agree that a good product coming out of a company with abusive practices behind-the-scenes is unlikely to be boycotted widely, but the company is still shady.
I'm curious if you use Uber because of the convenience or vehicles? I use Hailo for the convenience, but I'm curious if Uber is more convenient or you just prefer their vehicles and/or driver service.