Based on my experiences (which are certainly not comprehensive)...
New York: Letchworth State Park and Watkins Glen State Park are highly recommended. Watkins Glen does not list any sites as suitable for RVs longer than 30', but that is not really accurate; some of the sites are small, but some are perfectly suitable for a 40' RV as well and the access roads (at least the ones I've seen and been on) are not exceptionally tight or constricted. Letchworth I think has sites listed to that length. Both are stunningly beautiful areas.
Route 8 through the Adirondacks is a pretty road (not spectacularly so, but pretty) but might be somewhat steeper and curvier in sections than you would wish, particularly between Speculator and the Hague. It should be possible to safely drive it with your rig.
Pennsylvania: If you like amusement parks, there are several excellent ones in Pennsylvania. My favorite is Knoebels in Elysburg, which is a pretty large, rather old-time place. They have a couple campgrounds associated with it, one literally right next to the park and one a shuttle bus ride away. The one further away is definitely the nicer campground, but I prefer the convenience of being a brief walk from the park. Hersheypark and Kennywood are also top-notch amusement parks, and there are several other good ones.
Philly has many sites worth seeing: the Art Institute is world-class, the various historic sites, etc. The Campus Park and Ride is one possibility for "camping" when touring the city. Their web site is very forthright about the sort of facility this is (a secure parking lot with hookups).
Vermont: The Vermont state parks are nice but quite rustic (no hookups) and most of the sites and many of the access roads would be very tight or impossibly small for your RV. I'm rather limited at 32 feet.
There's a gaggle of parks around the Groton state forest, and they're all interconnected with hiking trails. It's a nice area, and there are hikes of various lengths and difficulties available. Owl's Head mountain has a really neat little stone CCC hut at the top and some good views, and is accessible with only a short walk (up a fair few stone steps) from a roadway.
Mt Philo is a nice easy hike or carriage road drive, and has a great view of Lake Champlain. Leave the trailer elsewhere for the road. There is a small campground in Mt Philo state park, but it would not be suitable for a big fifth wheel (and the carriage road to get to the top and to it would be very difficult if not impossible to manage).
Vermont route 17 across the Appalachian Gap (between route 116 and 100) would probably best be avoided with the trailer, though it's not technically impossible. It's very steep and has many very sharp curves. Vermont route 108 through Smugglers Notch (between Jeffersonville/route 15 and Stowe/route 100) should definitely not be attempted with the trailer; you would stand a good chance of getting physically wedged between the rocks. It is a fun drive without the trailer, and there are several varied hiking trails around the top of the notch. This is a quite scenic bit of road.
Camel's Hump has several trails up it and offers a tremendous view from the top on a clear day. Mt Ascutney is another great mountain for hiking (or driving most of the way up if you want a less strenuous hike) and has nice views of a different part of the state. The campground at Mt Ascutney state park has a few sites that I think would be suitable for your RV; calling the ranger directly would probably be your best bet.
On Lake Champlain, the City of Burlington has an adequate but not exceptional campground (with hookups) at North Beach. The beach is a very nice (and popular) swimming beach, and the Burlington Bike trail goes through the park, extending several miles along the lake. Apple Island Resort on South Hero is a nice private campground/marina/golf course on the lake.
The Shelburne museum is a large and eclectic museum, well worth a day's exploration.
New Hampshire: The white mountains are lovely. US2, US302, and the Kancamagus Highway (NH 112) are all entirely suitable for RVs. The Kanc in particular is a pretty road and has a number of short and not-so-short hikes along it. Sabbaday Falls is particularly nifty. US302 also has one or two impressive waterfalls, and Franconia Notch likewise. Do be aware that the area around Conway and North Conway, at the western edge of this area, is rather built up and traffic is often pretty congested and slow.
Canobie Lake (Salem, NH) is a fun older amusement park in southern New Hampshire, if that sort of thing is to your liking.
Massachusetts: Don't attempt to drive in Boston. Driving under Boston isn't too bad, but propane is not permitted in the tunnels. Navigating and driving the surface streets (with or without a trailer) is neither easy nor fun, and parking is not always readily available. Public transit (or tour busses) are, in my opinion, by far the best options. I usually catch the subway at Alewife, on the edge of Cambridge, which has a large parking garage attached to the station.
Some of the attractions worth considering in Boston include the Aquarium (very nice), the Science Museum (particularly known for their enormous Van de Graaf generator), the Museum of Fine Arts, and several historic sites.
