An interesting and thought provoking op-ed in The Hill outlines the issues, and asks the question.  The author, David Weisberg, concludes by saying yes, President Obama will likely pardon Hillary Clinton prior to leaving the White House.
(Via The Hill) […] We should first note that the Obama administration’s decision not to prosecute Mrs. Clinton would not bind the Trump administration. Until relevant statutes of limitations have expired, she could still be prosecuted by the new administration. It is possible in my opinion for Clinton to be prosecuted for either her improper handling of classified information on “home brew,” or allegations of “pay to play” arrangements between the secretary of state and donors to the Clinton Foundation, which could constitute bribery.
The statute of limitations for most federal crimes is five years from the commission of the offense; that would apply to the two categories relevant to Mrs. Clinton. Her tenure as secretary of state ended Feb. 1, 2013, so it is possible that the statute of limitations will not run until Feb. 1, 2018, more than a year after Mr. Trump takes office.

What looks like one question—will the president pardon Mrs. Clinton?—turns out, on analysis, to be two. The first question is: Would Mrs. Clinton wish to receive a pardon?
That question seems to be a proverbial no-brainer. Surely, any person who had been in federal government would be eager to receive a presidential pardon, because it eliminates even the possibility of federal prosecution. That looks like all upside and no downside.
But there is a downside, and it isn’t trivial. A pardon must be accepted by the person who is pardoned if it is to effectively stymie any prosecution.
Furthermore, there is solid legal precedent that acceptance of a pardon is equivalent to confession of guilt. A U.S. Supreme Court case from 1915 called Burdick v. U.S. establishes that principle; it has never been overturned.
If acceptance of a pardon by Mrs. Clinton would amount to confession of guilt, would she nevertheless accept it? A multitude of factors would go into her decision.
She, together with her attorneys, would have to decide how likely it is that the Trump administration would prosecute her, and, if they did decide to prosecute, how likely it is they would be able to prove she had committed crimes.
Since being elected, Mr. Trump has been remarkably warm towards the person he used to call “crooked Hillary.” But how confident could Mrs. Clinton be that the Justice Department, under a Trump administration, would not prosecute?
Prosecutorial decisions are supposed to be independent of political considerations, so Mr. Trump’s recent friendliness should not be controlling once the new Attorney General is in office.
If Mrs. Clinton believes prosecutors might be able to make a strong case against her, the value to her of a pardon increases. If she is confident that any case against her would be weak or even futile, the pardon has less value. (read more)