CoolNESs is the fastest NES emulator for the Amiga, it is also the least compatible because it gets most of its speed by taking shortcuts in the emulation. Most games do not run properly on CoolNESs.
A/NES has a bit better compatibility, but still has a lot of problems with graphics and some mappers, and is slower than CoolNESs.
DarkNES is a bit slower than A/NES but has much better compatibility than both A/NES and CoolNESs.
Well, to my memory both CoolNESs and A/NES have both been ceased in their development.
A/NES development has recently started again, the AGA version only though, I think.
If I ever get back into programming on my Amiga, I'll probably release a new version of DarkNES, and finally release my VIC-20 emulator.