In addition to the other answers (which have good points) I think another factor to consider is what the focus of the sentence is supposed to be.
Using は establishes that thing as the topic (central focus) of the sentence, so saying 「紅茶はコーヒーより美味しい」is specifically making a point about (black) tea: "Regarding tea, it is tastier than coffee"
However, using が does the opposite, it puts the focus on the「(コーヒーより)美味しい」part, and just says that tea is the thing which satisfies that condition (i.e. "tea" is the answer to a (possibly unspoken) question): "In terms of tastiness, tea is better than coffee."
I actually also don't entirely agree that the と思う part is completely irrelevant. It's true that is not a major factor, and the other points that have been made apply the same whether it is there or not, but when it is present there is also a slight nuance that applies to と思う as well, depending on whether は or が is used. This is because the topic (は) always applies to the whole sentence, while the subject (が) usually only applies to a particular sub-clause, so if you say 紅茶は that actually makes it the topic of not just 美味しい, but also the verb 思う too. What this means is that if you say:
That will be parsed as:
so you are basically saying:
I am thinking about black tea, and what I think about it is that it is tastier than coffee.
But if you use 紅茶が then that usually would only apply to the local sub-clause, so:
would be parsed as:
which says basically:
I am thinking in general, and I think that tea is tastier than coffee.
Of course, none of these are inherently wrong things to say per se, but which one actually makes sense or feels natural will depend a lot on the particular situation, for obvious reasons.