Not a lot of name chain hotels between Boston and Bar Harbor. One idea: they are building a new Hilton Garden Inn in Freeport, Maine that is opening for business right around now. That's about three hours north of Boston, three hours south of Bar Harbor. Three-star property, pool for the kids, breakfast buffet, don't know about suites but you can get two adjoining rooms. HGIs are great and Freeport is outlet city -- L.L. Bean and about 200 other stores to comb.
There is also a very good HGI in the Old Port section of Portland, but it can run very expensive ($200+). Other options: a so-so Holiday Inn in Bath, the Portland Jetport Sheraton, and a bunch of non-chain motels around Portsmouth Circle in New Hampshire, just across the Piscataqua River from the Maine state line.
As for your second need, between Boston and NY, I'd recommend Newport or Mystic Seaport, CT for an overnight stop. No specific hotels to call out, though.