My thinking has always been "Steam isn't going anywhere, so my games are safe." If Steam/Valve went under, I'd lose everything is bought... But the odds of that are pretty slim. Probably goes double for the App Store though.
I prefer Steam because I also have a Windows PC and games from this store usually can be installed on Windows and OS X (unless of course there is no Mac version or creators decided to sell it separately).
When I was going to buy my first games to my Mac I thought I'll buy from Mac App Store instead of Steam. But then I installed Steam and checked it offerings, and probably will buy most of my games from there in the future.
Weekly sales. There are really nice sales on games even for Mac
And when you buy the game you get a license that works on windows too.
Of course there's sales on MAS too, but not so often on new games. For example, Trine & Trine 2 were on sale on both, at Steam around 7 euros and at MAS for under 3 euros but those ain't so new games.
Then Borderlands were 6 euros on MAS where you got Borderlands 2 from Steam with that price.
I've bought around 10 games from Steam for my Mac from the weekly sales and when I look to MAS' prices I see I've made really great deals.
And some developers bring updates to Steam versions that MAS versions doesn't get.
Shortly: Both. But check Steam before you buy from MAS.