There was no one commander in chief of the United States forces in the Mexican-American War. Of course, the official commander in chief of the United States armed forces at any time is the President. The President during this time was James Polk was president.
The US sent two major armies into Mexico during this war. Each one was commanded by a different general. These were the main military leaders of the war. They were General Winfield Scott and General Zachary Taylor. Neither of these men was in command of the other and so neither of them could be called the commander in chief.
General Kearny marched into Santa Fe, New Mexico and conquered America's first foreign capitol. www.thesandovalsisters.com