Check M.E.S.S., it includes a colecovision emulator and it will work with game pad and other controllers.
I am waiting on my Ultimate InTV controller usb dongle thingy. Ordered it last night ’round 2am, groggy and sleepless night. Perfect timing for frivolous spending I have been contemplating to do for months… ;-)
Ps. I’m sure you can get ColEm going, might be much more work and don’t know how well the joystick support will work.
M.