"Which one is bigger?" would be ok as well? "Which is bigger?" sounds like it should be followed by options.
Or maybe the proper translation for my example in English would be "ποιό απο αυτά είναι τα μεγαλύτερα;"?
The original Greek phrase gives a neuter subject which would not be translated as 'Who'. You can go to Ποιος/Ποια/Ποιο from English, but when translating from Greek, 'who' is only an option when talking about Ποιος/Ποια and referring to people. Neuter is not an option when referring to people in English. Then, 'the biggest' is the superlative, which would be 'ο μεγαλύτερος' (or 'το μεγαλύτερο' in neuter) in Greek, so your suggestion is not correct in this case. :)
This would actually be superlative, not comparative. :) The sentence should have been "Ποιο είναι το μεγαλύτερο;" for superlative to work (Just like D_.. mentioned in her comment right above). ^.^