I'd never pick the Black Winter in a bright guitar; I love it in dark guitars, but it's too much in bright ones.
True, the BW isn't necessarily "darker" than the D-Sonic, but it's the better pickup of the 2 the OP mentioned for a lot of reasons.
There are limited options in the Duncan line when it comes to being "more powerful and a tad darker" than the D-Sonic. Alt 8 and Invader are probably the best standard production options. Custom Custom would indeed be warmer, but also much less powerful.
Personally, I'd be looking at the DiMarzio Pandemonium first and foremost. It has more power, a warmer voicing, and a similarly tight response to the D-Sonic. The new Jake Bowen "Mirage" also looks somewhat promising with its emphasized lows/mids and rolled off high end.
I also want to point out that the John Petrucci pickups have been steadily moving toward warmer, darker voicings with more power over the years. Basically, from brightest to darkest: D-Sonic > Crunch Lab / Illuminator > Dreamcatcher > Sonic Ecstasy. Any of those aside from the D-Sonic could be a move in the right direction. In fact, I'd put the Dreamcatcher or the Illuminator near the top of the list alongside the Pandemonium as my personal recommendations.
Edit: To the OP, have you tried flipping the D-Sonic around? It sounds slightly different depending on which way you orient the bar coil (i.e. closer to the bridge vs neck).