Biking north of Toronto to Newmarket

I would avoid the waterfront trail, partly because it's too slow and partly because it would take you far south of your Newmarket destination.

I don't know your starting point or anything about cycling routes in Hamilton. But if you can find a good route to Waterdown, it should be fairly easy from there. You could consider a route from Waterdown like Parkside Dr and No. 1 Sideroad east to Appleby Line, north to Britannia Rd., east to 8th Line (parallel to Trafalgar Rd but with less traffic) and north into Georgetown. Sorry I don't know Georgetown, so your on your own there. From just outside Georgetown, east on Mayfield Rd or Countryside Dr, north on Humber Station Rd to Castlederg Sideroad, east on Castlederg and King Twp 17th Sideroad to King Twp 10th Concession, north on 10th Con, east on 19th Sideroad and the Lloydtown-Aurora Rd., then north on your choice of Keele or Dufferin or even Bathurst into Newmarket.

Such a route would avoid most of the heavily travelled major roads, but by doing so also avoids a lot of things like convenience stores and bike shops. So be prepared to be self-sufficient, or have a support car at the other end of your cellphone. Good luck.

Only a bit flatter, but it does skirt the escarpment which is something...

Take Lakeshore as far as 3rd Line in Oakville, then north to Upper Middle Rd, and east on Upper Middle Rd to Sixth Line. Take Sixth Line all the way to Steeles and then jog left to continue even further north on Sixth to No. 5 Sideroad. Go east on No. 5 Sideroad all the way to Heritage and then north on Heritage to Old School Rd. Take Old School Rd East to Humber Station and then go north to Castlederg Sideroad. Follow Castlederg east to 11th Concession and then go north to 19th Sideroad. Head east again to Rebellion Way (a T-junction) and turn right to follow it east again where it becomes Lloydtown-Aurora Rd (RR 16). At Jane St you will need to head south about 1km to continue on RR16 to the south end of Newmarket. Absolutely no roadside services from the north end of Oakville to Pottageville (about 75 km.)

Depending on where you start in Hamilton and where you plan to end up in Newmarket you are looking at 130 to 160 km. Traffic depends on time of day, of course. During the week 3:30 to 5:30 is the worst time to ride out in the burbs. For those two hours there is no such thing as a quiet country road.