The Northern Tier uses the Erie Canal Trailway from Lockport NY eastward to Palmyra NY. The section from western Rochester to Pittsford is paved, and suffers from an ongoing problem that comes and goes: tree roots causing sharp bumps in the pavement/tarmac. Unlike a rail trail, canal trails are not lined with deep ditches and built on soil that was polluted for decades with coals from steam locomotive fireboxes; they are on good dirt with minimal drainage and lots of water nearby. Thus, the trees actively grow roots and cause upheavals in the pavement. (This is not a problem on the unpaved parts.)
When the pavement gets too bumpy the Canal Corporation scares up some money and repaves it. This alternates as sections get bumpy. Right now, one section has gotten bumpy enough that you need to exercise caution: between Kendrick Road and East Henrietta Road. I would still recommend using the canal trail, but watch your speed and avoid the bumps if you can.
The road alternative over this part of the trail, NY Bike 5, is a horrible route. It uses Elmwood Avenue and Monroe Avenue, both of which have no bike lane and four lanes of medium-to-heavy traffic. Drivers on western Elmwood, around Strong Hospital, seem to always be impatient and intolerant of bikes. So stay on the trail, but stay on your toes.