In my opinion, they both share the same meaning of "~, isn't it". However, it seems that they cannot be used interchangeably. For example, in the following sentence, according to my mock exam textbook, ではないだろうか is correct for __ but not だろうか .

ラブレターや海外からの絵葉書をメールで代用するのはおそらく無理 __。

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    +1 but I do wonder where you learned that the two shared the same meaning. They do not. – l'électeur May 17 '16 at 14:04
  • I feel that だろうか has more a doubting feeling, whereas ではないだろうか emphasizes more that something is probably true. – Locksleyu May 17 '16 at 14:59
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    「ではないだろうか」は、「だろうか」よりも「だろう」のほうにより近いと思います。 – Chocolate May 17 '16 at 15:00
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    Only ないだろうか means "~, isn't it". – broken laptop May 17 '16 at 15:27

In the descending order of certainty:

  • ~だろう = "I think (some clause)." The speaker thinks the clause is probably (or almost certainly) true.
  • ~ではないだろうか = "I think (some clause), isn't it?" The speaker thinks the clause is perhaps true, but he's less certain as compared to the first sentence.
  • ~だろうか = "I wonder whether or not (some clause)." The speaker doesn't know if the clause is true or false. You cannot add 恐らく to this sentence because the speaker is totally unsure.
  • ~ではないだろう = "I don't think (some clause)." The speaker thinks the clause is probably not true.
  • 彼は(恐らく)大丈夫だろう。 He must be okay.
  • 彼は(恐らく)大丈夫ではないだろうか。 I think he is okay.
  • 彼は大丈夫だろうか。 I wonder if he is okay. / I'm worried if he's okay.
  • 彼は(恐らく)大丈夫ではないだろう。 He must not be okay.

In the example sentence, the speaker is saying "It's probably impossible (無理) to use e-mails in place of ...", so 恐らく無理ではないだろうか is the correct phrase. 恐らく無理だろう is equally fine. The existence of the word 恐らく is what makes ~だろうか wrong. You can't usually say "I wonder if he is probably fine." in English, either.

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