It's hard to compare them directly in their power:
Hillary Clinton is the Secretary of State. That's the person appointed by the president to carry out his foreign policy. She's in charge of international relations, treaty negotiation, diplomacy, and in general she's the most powerful person besides Obama for foreign policy.
Nancy Pelosi is the Speaker of the House. She is an elected representative to the House of Representatives from San Francisco and the members of the House then voted her to be their leader. As such, she has a lot of power to make laws. She has a lot of control over what potential laws come to a vote in the House and she uses that to negotiate for her positions in different laws.
Pelosi's role is important, but she has to share power a lot more. There's also Harry Reid, the Senate Majority Leader, and all the other members of Congress, who have just as much voting power as she does and can decide to vote her out if they don't like her. Clinton, on the other hand has a great deal of freedom in how she chooses to handle US foreign policy, but she ultimately serves at the pleasure of the president and if she disagrees with Obama she has to either do what he says anyway or he can fire her. Most of her power comes from her ability to advise him and influence his decisions.
The only way I can think of to compare directly is in the line of succession. If the President dies or resigns, the Vice President become President, but if he can't do it, Pelosi becomes President, making her second in line. Clinton is 4th in line, as the President Pro Temp of the Senate Robert Byrd is 3rd. In that regard, Pelosi is more powerful. Really, though, that doesn't mean much. There's no good direct comparison.
EDIT: I'm not exactly sure of the parliamentary procedure, but I believe they can vote no confidence and change their leadership at any time. She would remain in congress unless and until her constitutents in San Francisco vote her out (members of the House of Representatives are up for re-election every 2 years), but each house of Congress chooses it's own leadership. That's not likely to happen, though. The Democrats have a substantial and solid majority in the House of Representatives and Pelosi enjoys pretty strong support among them. Generally, whoever gets the majority vote for their party leadership gets nearly all of their party's vote for the leadership in Congress (when that doesn't happen, it's a big deal), so as long as Pelosi has the majority of the democrats behind her, she'll remain the Speaker of the House.