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アザラシは寒い海にいることが多い動物です。
The アザラシ is an animal that often lives in cold seas.

I'm not entirely sure that 'often' is the right translation here. How does this sentence differ in meaning/nuance from:

アザラシは寒い海によくいる動物です。

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In your specific case, 寒い海にいることが多い and 寒い海によくいる are interchangeable, and they both mean "to be often seen/found in cold waters." (Note that these sentences does not mean individual earless seals often migrate from cold waters to other places.)

In general, ~ことが多い and よく are not always interchangeable. ~ことが多い means:

  1. often; frequently
    • 日曜日はテニスをすることが多い。 I often play tennis on Sundays.
  2. there are many things to ~
    • 日曜日はすることが多い。 I have lots of things to do on Sundays.

よく also means several things depending on the context:

  1. often; frequently
    • 彼はバナナをよく食べる。 He often eats bananas.
    • ここでタクシーをよく見る。 I often see taxis here.
  2. well; much; intensively
    • 彼はよく食べる。 He is a good eater.
    • あのタクシーをよく見ろ。 Look at that taxi carefully.

That said, I think よくいる and いることが多い are almost always interchangeable.

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よく and ~V+ことが多い are basically the same meaning. The difference would be sentence construction.

The following sentences would have the same meaning:

秀樹さんは図書館に行くことが多い。Hideki goes to the library often.

秀樹さんはよく図書館に行きます。Hideki often goes to the library.

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アザラシはよく寒い海にいる Seals spend much time in the cold ocean.

アザラシは寒い海にいることが多い Seals spend much time in the cold ocean (are in the cold ocean much).

Incidentally, the sentence does not say that seals ‘live’ in cold seas, but that seals ‘are in (found in)’ cold seas. Also, somewhat of a quibble, but to say ‘ocean’ instead of ‘sea’ would be more appropriate.

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