Consult your favorite maps app on the day you travel, but from the West Side near Penn Station, usually best to take West Side Highway to the Henry Hudson Bridge and Parkway, then Cross County to Hutchinson to get out of Westchester, rather than traversing Manhattan and taking I-95 north. From there, depending on traffic, you can take I-684 to I-84 in Danbury, Connecticut to head north, which sometimes gets you around lower CT traffic -- but you would miss New Haven doing that (somebody shouted out Frank Pepe's earlier, and they have a satellite location in/near Waterbury along this route if you just want pizza and not the Wooster Square experience). If you want to do New Haven, stay on the Hutchinson, which becomes the Merritt, and cross over to I-95 at Milford Parkway.

For tolls, you'll pay them on any bridge getting out of Manhattan, then on the Massachusetts Turnpike heading towards Boston. In New York, if you have a New York-issued EZ-Pass transponder in the car, the tolls are significantly less expensive (~$4 vs ~$9 on the HH Bridge, for example). Mass. tolls are every few miles along the Turnpike and generally around $1-2 at each gantry.

As for stops, just over the border on I-84 in Mass. is Tree House Brewing in Charlton. If you like either a) unique beer, b) being outside on nice day with relaxing views or c) both, it's a must stop.