I am not a native Japanese speaker. I would probably put it like:
化学を勉強するのは日本語と英語とどちらの方が簡単ですか？
But I am not sure what is the proper way to combine the particle で with どちらの方が, which I think is the main point of your question.
I know this is about how to ask the question in Japanese, and not the question itself... but why would it be easier to study chemistry in one language or another? Assuming you knew both languages equally well.
maybe: 化学を勉強するなら日本語と英語のどっちで勉強しやすいでしょう？
For Leebo: i personally find the amount of greek used in english quite a bit confusing so I do think it can be easier to study science in a language that has a naming system that is more intuitive to you personally. Not sure if japanese is the one but everyone is different, i guess.
I want to say "In which language is chemistry easier to study, English or Japanese?" Does this make sense？
化学を日本語か英語で勉強する事とどちらの方が簡単ですか？