My sister lives in Boston, so I've made this trip frequently-- even when the kids were little -- it's actually not that bad (and I hate driving). My advice is to avoid 95 as much possible; instead, once you're in NJ, switch over to the GS Parkway or I287, either of which will take you to the I87/NY Thruway. Follow that to I84 across the Hudson at Newburgh, NY, then stay on 84 through Connecticut to the Mass Turnpike to Boston.
For an overnight stop there are plenty of hotels along the way with pools. An Embassy Suites would work well with two little ones -- most of these have indoor pools, so you can give the kids a swim and dinner, then tuck them into bed in the bedroom while you watch a movie or read in the sitting room until your bedtime. For a little more money, there's actually a really nice outdoor pool at the Hilton at 287 and NJ10.
If you want a little more of an outing, rather than just the overnight stop, one fun option might be Storm King Mountain, an outdoor sculpture park along the Hudson and just off the NY Thruway. Your kids can run and marvel over the huge sculptures and tire themselves out. Again, there are plenty of hotels along that part of the Thruway, so it shouldn't be a problem to find one, though I would make a reservation just for your peace of mind.
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