Earlier quoted context omitted.
Obama has said that the two cases are different in that Manning has gone through the legal system, sentenced, and serving time, whereas Snowden is in a country that doesn't have an extradition treaty with the US and hasn't been tried under the US legal system.
Specifically, one cannot be pardoned or have a sentence commuted of a crime one has not been convicted of. Snowden has not been convicted nor even tried for any crime. It's impossible for Obama to do anything about his situation.
This was the case with Ford's pardoning of Nixon, as well as Carter's pardoning of all those who avoided the draft during the Vietnam war.