If I were just making a simple statement about today's weather, the stress would fall on "hot". However, it wouldn't be stressed particularly strongly.
I would stress "day" only if I were disagreeing with someone or refuting something they had said.
John: Wow, it's a really hot week, isn't it?
Helen: Well, it's [certainly] a hot day, but yesterday was pretty average and Thursday night was quite cold.
In reality, I wouldn't say "It's a hot day" to refer to today. I'd use that word and say "It's hot today". I would use the same phrase in the dialogue above and the stress would very clearly be on "today".