I translate it to
The big building is visible over there.
Can I also translate it to the following?
The big building over there is visible.
In other words, can I assume that 向こうに is a relative clause for 大きなビル?
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It's impossible to parse it as a relative clause because there is only one verb/adjective (ie, 見えます) in the whole sentence. As a rule, each sub-clause must have a verb/adjective.
So the real question is: "Which word this 向こうに modifies?"
向こうに can only modify a verb, and 向こうの modifies a noun. Both can be translated as "over there" in English, but you need to distinguish them in Japanese.
Since 向こうに can only modify a verb, it modifies nothing but 見える at the end of the sentence. So your first translation is the correct one.
If you say 向こうの大きなビルが見えます, that is grammatically correct and this 向こうの modifies ビル ("the building over there"). But semantically, saying "a big building over there" already means the speaker and the listener can see it, so "A big building over there is visible" sounds awkward to me.
For example, 「向こうにある大きなビルは赤いです。」 is a semantically valid sentence which uses a relative clause (向こうにある modifies ビル and ある is a verb).
向こう is grammatically a noun, so the sentence you have can really only be parsed as ＡにＢがする → （向こう）に（大きなビル）が（見える）. If you want it to be parsed as in your second translation, I think you have no choice but to choose something like 向こうにある（あの）大きなビルが見える.
From my experience, there is no problem with either of these translations. Although 「向こうにある大きなビルが見えます」is probably better. Here are a couple others which might be natural in context...
As long as you keep the information the same, i.e.
at other side / big building / becomes visible
you're pretty free to translate it in a lot of different ways, as long as you don't contradict any information in the context.