Easily Beast Wars. While I may be biased due to it being the Transformers I grew up with, I've rewatched it since then, and it really does hold up as a good show.
As for Beast Machines... I have mixed feelings. See, when taken on it's own merits, as a stand-alone show it's actually not that bad. The action is good, the CGI used to make it have actually stood the test of time (even better than than Beast Wars), the villain is threatening, and it has a very different flavor to any other Transformers incarnation, even it's prequel.
But, unfortunately, that's actually the main, crushing flaw with it: As a sequel-series, it fails about as hard as it can possibly fail. When making a sequel-series, there are alot of things you can change, but there are two you really, really shouldn't change: Characterization and tone. Machines changes both... to disasterous results. Every returning character undergoes a massive personality shift, and Cheetor is the only one who's change is actually positive, as it actually advances his character development from Beast Wars. Even Megatron himself just seems like a completely different character. He changes from a slightly campy, ruthless schemester to a cold, mechanical despot with only one single-minded goal.
And then there's the issue with tone. Beast Wars had a very militaristic, light-hearted tone. But Machines is more like Sonic Sat:AM without the humor. Well, except for Jetstorm, but he's the lone exception.
I could really go into an in-depth, essay-long post about the pros and cons of Beast Machines (actually, that's not a bad idea for a thread), but the point is that Beast Machines probably isn't as bad as you think it is, but you've also got every right to hate it.