From around the PA/NY border, break off and head north toward Ithaca. When I rode the Northern Tier, it actually went through Ithaca I think but that was in the 80s and ACA keep altering the routes a little to keep them viable. If you don't mind riding on crushed gravel/chat/stone dust, you could break off at Poughkeepsie and head toward Albany and connect with the Erie Canalway Trail (very rideable on touring tires) then break off that around Weedsport and head south to Ithaca.
For each state you are doing your own route, check the state's department of transportation for a state bicycle map, traffic count maps, and county maps. You can use Google to see if any bike routes exist but take those with a heavy dose of salt. Try to go to streetview and see what the road/trail is like. I try to stay on roads with less than 2,000 vehicles per day (prefer 1,000) but that may a bit difficult in the east. You typically give up flatter roads, possibly shoulders, and more services for much less traffic and more scenery and "character". New York has a pretty good site.
Due to the heavy traffic in the east coast corridor and the amount of research required to create a safe route, I would strongly consider following the Atlantic Coast Route IF you want to visit the major cities. Otherwise, swing west from Front Royal through western MD and central PA on your own route.
Whatever you choose, have a great ride!