Two comments -
EZ-Pass - works on all NYS toll bridges, tunnels and the NYS Thruway - also works on Mass Pike.
Metro North - I also agree with the Metro North comment. There are tons of decent yet reasonable hotels along the train line that runs to Poughkeepsie. You can park the bikes at the hotel and take the train down and back for a day of sightseeing.
I am also planning to ride to Newfoundland this July but don't know dates yet. It all depends on when my girls go away to summer camp. But I have the whole winter to dream and plan.
Good luck on your trip.