My vote goes to Amaranth (3329 W. Lisbon). I believe they serve Anodyne Coffee (if not, then it's Valentine), and the baked goods and other foods are superb.
Amaranth Bakery and Cafe
I like Anodyne's coffee more than Colectivo's, but hate that both places use paper cups unless you specifically request a mug or glass. Colectivo is more versatile, though: Anodyne doesn't always have decaf coffee on hand, so cannot always make decaf lattes, etc. (just Americanos, which I'm not fond of). (Yes, I'd rather not drink decaf, but caffeine sometimes makes me dizzy, so I have to drink it sparingly.)
Colectivo has better baked goods and food options. Anodyne pretty much just sells Saran-wrapped cookies and muffins from other outfits (like East Side Ovens, not one of my favorites), though the Bay View spot has tasty wood-fired pizzas. Colectivo's food isn't amazing, but it's serviceable. Amaranth is much better overall.
I've had good and lousy service from Colectivo and Anodyne. Generally, Colectivo cafes are good places to find an empty seat or unused table and do stuff, though some locations could use more outlets (some window-side seating bars have none, amazingly). I like Anodyne's independent feel; Colectivo seems too corporate and slick these days. Overall, I might give a slight edge to Colectivo (vs. Anodyne), but just barely.