Whiting won with a mark of 72 feet, 11 1/4 inches Sunday on the fifth of his six attempts.
"I knew I was on my way up," Whiting said. "I just threw better than everybody else. I'm a lot stronger than I was last year. I'm a lot more ready. I'm just getting stronger and I think that just comes with the age."
The 27-year-old Whiting had the fifth-best indoor mark in the world, about 17 inches shy of the world indoor record set by American Randy Barnes in 1989.
He qualified for the U.S. team for the world championships in Poland on March 7-9.
"It just happened that you had to throw far to be able to do it," Whiting said. "I had been doing some things wrong and I tried to fix it the last few meets. The other guys have proved that no mark is safe in U.S. shot putting."
Seventeen-year-old Mary Cain successfully defended her title in the 1,500 meters, winning in 4:07.05.
She credited the partisan crowd.
"I have a fan base in New Mexico," said Cain, from Bronxville, N.Y. "Who would have thought? I really wanted to do it for them."
On a speedy track, she said it helped to overcome the mile-high elevation.
"I'm glad it was a fast pace," Cain said. "I would have been fine if it was slower. I would have been able to keep my cool, but this just gives me more confidence that I can run a 4.07 at altitude. I still feel pretty good."
Omoghan Osaghae won the 60 hurdles in 7.553 seconds, two-thousandths of a second ahead of Dominic Berger and six-thousandths ahead of Terrence Trammell.
"It was such a great field as the times reflected," said Osaghae, who has been battling a series of ailments. "I'm just beyond blessed to be in this position because in no way, shape or form a month ago was USA in the realm. It was just getting through practice and getting ready for outdoors without having something flare up so to be here and being crowned champion and being able to defend it is just, I don't even know. It's more than amazing."
Mary Saxer won the women's pole vault with a personal best of 15-5 1/2, beating Olympic gold medalist Jenn Suhr by 2 inches.
"I literally am kind of speechless," she said. "Beating Jenn is amazing, but I know she didn't have her best day, too. But it's my first national title. So I'm going to soak up the moment."
Nia Ali won the women's 60 hurdles for the second straight year, finishing in 7.8 seconds.
Lopez Lemong won the men's 1,500 in 3:43.09, rebounding for a disappointing showing Saturday in the 3,000.