Both pedals are excellent choices IMO. They are completely different animals, though.
In the end, the choice comes down to wants and needs regarding cost and functionality. The Stomp is technically a much deeper design featuring advanced programming and external expansion of function if you want to go there. The B6 is less expensive and caters directly to bass-specific needs, designed with simplicity in mind for those who don't require deep function, and want to hit the ground running with solid amp & effects choices available.
The Stomp has the Line 6 Helix legacy modeling going for it, which is great for those who also use guitar amp modeling.
Functionally, the Zoom B6 is designed for ease of use and simple programming, whereas the Stomp his highly configurable and programmable, especially with MIDI implementation for external control pedals.
If floor space is an issue, the Stomp is much smaller...good for some reasons, not good for other reasons.
If XLR included connection and DI functions matter to you, then the B6 did a nice job with their implementation, with the switched dual input (with selectable impedance for each) to boot.
The B6 has more switches and the touch screen allows you to get around pretty quickly for on-the-fly editing. I would note the 4 switch limitation for switching effects/banks/patches...better than the Stomp, but not utopia by any means.
I found the Stomp to be awkward without having the software editor handy, and using only 3 switches to navigate in live performance is a huge negative for me and required an external footswitch to be functional for my needs at the gig. The newer Stomp XL solves this, with requisite cost bump.
Core sound-wise, I'd say the B6 is at least on par with the Stomp bass amp models (dare I say some are better? Yup, I do.), and each have good choices available to cover pretty much any genre. If parallel path tones are your thing, then the Stomp provides this, whereas the B6 IMO just gets you to satisfying tones quickly without much programming fuss.