How's it going is synonymous with how are you doing. How's it coming is usually used to refer to a specific action, rather than the persons emotions or physical state. Ex. How's it going? Good, I've had a good day. How's dinner coming? It's almost ready. Of course, if they know what you are talking about it, you can replace 'dinner' with 'it'.

it's going great and coming along fine :P

Both mean nearly the same thing, an enquiry about how something is progressing