AFAIK there is no custom made IDE for Atari ST crossdevelopment, only toolchains.
I personally use Qt creator (thanks mfro for the suggestion), Vincent Riviere's crosscompiler toolchain and Hatari as a debugger.
Hatari does not plug in so you cannot use the IDE to debug but otherwise it is a terrific environment.
Simon Sunnyboy/Paradize - http://paradize.atari.org/Stay cool, stay Atari!
1x2600jr, 1x1040STFm, 1x1040STE 4MB+TOS2.06+SatanDisk, 1xF030 14MB+FPU+NetUS-Bee