Companies I can think of are...
Hyperion: have been fairly prolific in the last two years, and still have projects in development. They are involved in Warp3D and the new AmigaOS. They specialise in PC game conversions, though, so...
Apex Designs, producers of Payback, may also be considered active.
Pagan Games handled the conversion of Earth 2140 to Amiga, and have an interesting-looking RPG in development.
Digital Dreams produced Wasted Dreams and Codename: Hellsquad. Their website mentions WD2, but has not seen an update for a long time.
Titan Computer develop and publish games for the Amiga.
A site which covers new releases (with accent on 3D) is
Amiga Extreme. Not a lot of news lately, bar Payback stuff. One news item regards Maim & Mangle, an original Amiga 3D space thingy. Currently being developed by
World Foundry.