Even though I'm a huge Darkwing fan and run one of his best and most extensive sites.... i confess, I do think I like DuckTales better. I was always a fan of DuckTales, have the world premier on tape. Assuming the tape hasn't decomposed by now.
Ducktales was a comic book before it was cartoon. Donald Duck had a bigger part but one of the best character was new for the TV series, Launchpad (he's my fave character and I'm sad he's not around anymore) along with Mrs Beakly and Webby.
I collect Simpsons comics and I was delighted when they did a parody of Ducktales comics. Mr Burns was Scrooge, Homer was Donald, Bart, Lisa and Maggie were Heuey, Dewey and Lewie, Professor Frink was Gyro and Snake (with his cousins) were the beagle boys but they were called the jailbird boys.
Really, they're two different genres. Ducktales is more of the younger adventure show, while Darkwing Duck was a bit more skewed to the older audience, and much more superhero/action focused. The closest Ducktales got to that was GizmoDuck.
So I'd say apples and oranges... but in the end Darkwing comes out on top for me.