The 20-year-old goalkeeper is held in high regard at the DW Stadium but other, more experienced, options are currently favoured by boss Roberto Martinez.
That has allowed Nicholls to go in search of game time elsewhere, and he has excelled during a stint in League Two.
The youngster has kept 15 clean sheets during his time with the Cobblers, helping to fire them into automatic promotion contention.
Nicholls will be looking to end the season on a high by helping Northampton into League One, and Boothroyd hopes the England U20 international will then return to the club for the 2013/14 campaign.
He said: "Wigan are happy with Lee's development and I have to say I'm absolutely delighted with how he's done.
"He is getting better and better and we'd love to have him for another year."