Boucher, who is visiting New Delhi to hold talks with Foreign Ministry officials as part of his first swing through the region since being named to the post in January, said Washington had an "important relationship" with Pakistan, a frontline ally in the US war on terror.
"Obviously, there are difficulties with extremists in Pakistan. We face a threat, India faces a threat. The Pakistan government faces a threat," he said.
"But we are all in this together. The only way out of this is together."
He was confident the US Congress would approve a major civilian nuclear deal with India, but said it could take a year for implementation.
Boucher said he believed the Congress would clear the agreement "because it is part and parcel of a new relationship with India. People want to support it."
"We are moving full speed ahead."
US opponents say the deal abandons longstanding non-proliferation rules, complicates efforts to curb the spread of atomic weapons, such as in Iran and North Korea, and could spur India to expand its nuclear weapons arsenal.
Boucher informed a business group that he hoped there would be a Congressional "vote in a few months from now", but cautioned full implementation of the agreement might take "maybe a year at best".
Under the deal, energy-starved India would gain access to long-denied civilian technology to help in fuelling its fast-expanding economy in return for placing a majority of its nuclear reactors under international inspection.
"There are a lot of pieces of this puzzle (to put together)," Boucher said.
In addition to Congressional approval, the 45-member nation Nuclear Suppliers Group must also sign off on the agreement.
The deal faces other hurdles such as an accord on inspections between India and the UN's nuclear watchdog, the International Atomic Energy Agency (IAEA).
Boucher, however, said lawmakers were coming around to accepting the deal described by US Secretary of State Condoleezza Rice as a key element of "a partnership that will become one of the most important we have with any country in the 21st century."
The pact would end three decades of isolation under which India was refused help for its civilian energy programme after it first tested a nuclear weapon and refused to sign the nuclear Non-Proliferation Treaty.
Boucher, who heads home next week, rejected media speculation Washington wanted better ties with India as a counterbalance to China's growing regional might, calling this "zero-sum thinking too simplistic."
India and the United States were on opposite sides of the fence during the Cold War, but ties have warmed sharply since.
"Good relations with India do not come at the expense of good relations with China," he said. "Both can be responsible stakeholders in the international system (and) are welcome and important partners of the United States."