Knighton started 11 games for Vancouver in 2013, compiling a 6-3-2 record before losing the No. 1 job to David Ousted midway through the season.
The 28-year-old Knighton, who began his professional career with the Revolution in 2007, joined the Whitecaps in January 2012 following a season with the Carolina RailHawks of the North American Soccer League.
In two campaigns with Vancouver, the Hickory, N.C., native was 13-7-7 with eight clean sheets in all competitions.
Knighton would have been eligible for Thursday's MLS re-entry draft after the Whitecaps declined his 2014 contract option last month.
Knighton will have a chance to compete for the starting job with New England following the retirement of veteran starter Matt Reis.