I wouldn't by either at the moment. The AmigaONE is just a Linux box without OS4, and I'd wait for OS4/A1 reviews before buying a Pegasos.
Both are overpriced compared to an x86 board, although may compare favourably with a Mac. IIRC the A1 can beat the Pegasos at benchmarks, but the Pegasos II will be better than the Pegasos - but it's not out yet. Don't count on an OS4 kit for Pegasos - you could very well be disappointed.
So I'd wait around for a bit. Try out a Pegasos and an A1/OS4 if you can. And ignore people who tell you to get their solution without any good argument to back them up. I'm currently waiting, but I've decided on the A1 route myself.