I think some of Ecclestone's stories were pretty dark. Tom Baker's stuff could be scary but I wouldn't describe it as especially dark, so to speak. Although to be fair there's so bloody much of the Baker era that it's hard to keep up. Nothing springs to mind, though, at least compared with the Tennant-era stories like Last of the Time Lords. The closest I can think of is a story called
Seeds of Doom, but even that's probably more intense than dark. I'd say the Baker era was perhaps a bit heavier on the pure science than you tend to get with the Tennant-era which, in comparison, seems more psychologically than scientifically complex.
Essentially, I think they both appealed to different audience needs at the time. So if you're looking for dark, you're probably best off simply sticking with the reboots and if you fancy more full-on action, droll humour and mad scientific ideas, have a look at some of Tom Baker's stuff.