A couple of options on the NFCT come to mind, the first being the Allagash Wilderness Waterway in Maine, from Chamberlain Lake to Allagash Village. The Allagash gives you about 90 miles of lakes and river, ample campsite options, short easy carries, and a few miles of easy Class II whitewater through Chase Rapids.
Another possibility would be to paddle the Moose River Bow trip and continue down the Moose River past Jackman, Maine to Moosehead Lake. The NFCT intersects the Bow River trip at Spencer Rips. The Bow trip is famous for being a river trip that runs in a circle (with a portage to close the loop). The Moose River below Jackman is mostly lakes and easy river travel, with a few miles of whitewater below Demo Bridge, and a new portage trail that bypasses some of that whitewater.
A final option would be to paddle the first two NFCT map sections, from Old Forge to Saranac Lake, roughly 90 miles. Camping reservations are recommended well in advance on Upper and Middle Saranac Lakes. That’s a trip that I prefer in the off season, before Memorial Day or after Labor Day, more or less.
You could also consider paddling the Missisquoi River from Mansonville PQ (or Richford, VT) down to Lake Champlain. That takes you through a northern working landscape of mountains, forests, and dairy farms, and the Missisquoi National Wildlife Refuge at the end. Happy paddling! – Kalmia