"It", "This" and "That". They're all synonyms, they all mean the same, they are all interchangeable, so why is sometimes one of the forms more preferred than the others? They are not so interchangeable after all, are they? There are subtle but significant differences between them. For instance, you might prefer to use "this" to things closer to you and "that" to things further away from you.
In Portuguese it is the same thing. "This" means "Este/Esta", and "That" means "Esse/Essa", and "It" means... well, "It" doesn't mean anything. It's simply ignored/removed/brushed away. They are also all synonyms, all interchangeable, but there are subtle differences between them. And there is a direct correspondence between the English words and the Portuguese words:
It is a good question - É uma boa pergunta
This is a good question - Esta é uma boa pergunta
That is a good question - Essa é uma boa pergunta
It is good for you to use and learn the direct translation of each of these words, even if they're all synonyms. It will make you acknowledge these subtle differences in the future.
Bom is masculine (goes with masculine nouns), boa feminine. If you just say "good", without a noun, I think it's usually bom, unless a feminine noun is implied. For example, if someone shows you a painting of theirs, you might say "É boa," where "pintura" is implied.