I should confess I haven't been looking very hard; I asked around on Twitter a few weeks ago, and I've done a bit of Googling and browsing Duotrope, so I bet I've missed plenty. (Not checked Litmags, Ralan or E-Zines, for example. Not looked at the Writers' and Artists' Yearbook.) But I thought I'd post the results of my first trawl to see what others can add.
Here's the preliminary list of small or indie presses who seem to have interest both in YA novels and in speculative/weird fiction (except where noted, I've not always yet been able to ascertain that they have published anything that is both at once; bolded titles seem the most focused on the combination in question).
- 4GenresPress (unclear what focus, but website lists both speculative and juvenile)
- Bell Bridge Books (Southern): "fantasy, horror, young adult, mystery"
- Big Mouth House (YA imprint of Small Beer Press)
- Bold Strokes Books (includes LGBT, speculative, and YA)
- Coteau Books (Canadian writers)
- Cyberwizard Productions: includes speculative and other genre lines, and a children's books line
- Diversion Press
- Drollerie Press: fantasy and genre books including "Kettlestitch" YA imprint
- Eternal Press: erotic and paranormal publisher including a YA line
- Etopia Press: focus on erotic and romance, but strong speculative holdings and a YA line
- Helm Publishing
- Medallion Press (young adult imprint)
- Mundania Press: will consider YA if in their target genres (esp UF/PR)
- Nightfall Publications: horror/paranormal/genre; seems to include YA line
- Sumach Press (feminist and inspirational books)
- Tu Books (an imprint of Lee & Low): "fantasy, science fiction, mystery--diversity for children and young adults"