Note that if you want to develop with an existing MINIX system, Atari ST emulation is robust enough to handle MINIX, including hard drive support, so you could install a full MINIX ST system. The executables produced are compatible between the ST and Amiga versions (unless they use some specific hardware, obviously). ST can work as an excellent cross-development platform.
In terms of more "modern" compiler, you could check the ACK compiler.
http://tack.sourceforge.net/
Version 5.6 is relatively modern, it has 68k as a target architecture, and it can compile old non-ANSI code.