Now, a year-and-a-half off chemotherapy, he's active and well "and that's all you can hope for, every day", Ms Thomson said.
She and Lincoln were at the golf tournament raising money for the Child Cancer Foundation, a charity that receives no government funding.
Despite the wet weather, 36 golfers attended the first of what is hoped will be an annual event.
Ms Thomson handed around her son's "beads of courage" for all the players to wear.
Each bead represents medical steps Lincoln had endured along his cancer journey.
"Each hospital stay, blood transfusion, time in theatre - every procedure," Ms Thomson said.
"He's got three-and-a-half years worth of beads - that's as long as his chemo went for."
Ms Thomson said they had been the toughest years of her life.
"It's just your worst nightmare, really.
"Our journey was full of hospital visits and lots of travelling, lots of chemo and lots of seclusion because we couldn't be around anybody in case Lincoln got sick.
"He's been incredible through the whole thing. He's been my strength, not the other way around."
During this time, Ms Thomson fell pregnant with her second child which, she said, helped them through the challenging time.
"Life wasn't just about cancer - we had another focus and that was Lincoln's younger brother."
The Fernridge School student this year celebrates his first complete year at school without any interruptions.
Ms Thomson said her son had been "an absolute soldier" throughout his extensive treatment.
"He didn't complain once. The only thing he ever said was, 'Why do I have to take so many pills?' Other than that, he just rolled with everything.
"I'm very proud of him."
The charity golf tournament was organised in just three weeks by friends of Lincoln's family - Thomas Rimene and his wife, Jess, from Masterton.
Mr Rimene, a member of the Mahunga Golf Course, said he had been inspired by "the little fella".
The day teed off at 10.30am with rounds of golf, and later on there were raffles and an auction.
"The whole lot goes to children with cancer," Mr Rimene said. "We've had lots of sponsorship from generous businesses and individuals in the town."
The couple had been "amazing", Ms Thomson said.
"We're so grateful that Thomas wanted to do this off his own bat.
"So much time and effort really touches your heart."
The money raised will help support other families going through similar experiences.
