Great call on the Cloisters and the Ferry, Webster, althought the Cloisters will require a lot of walking. Dylan's Candy Bar is fun, but if you want REALLY GOOD chocolate, and are inclined to get to Brooklyn, head just over the bridge, in Dumbo on Water Street (which is cool because there is a park between the Brooklyn and Manhattan bridges with sweeping views of lower Manhattan and it has a boardwalk and even a little beach that sits right on the river). On Water Street which is across from that park, you get a funky feel for an old neighborhood that has gone from abandoned to thriving. It still has original cobblestones from the 1800s. Some old pre civil war buildings and warehouses, some which have been taken over by art galleries, a theatre, etc. and lots of creative types of business--P. Diddy, etc. And halfway down the block is Jacque Torres, which is a world famous chocolatier. It's the best chocolate I have ever tasted. You can actually look through the window and see them in their pristine white outfits making the chocolate. I don't eat chocolate anymore, but when I did, this stuff was as sinful and good as it gets. Have a cup of their hot chocolate while you are there (if it is still warm, go for the frozen hot chocolate). It is amazing. From there, just walk south to Old Fulton and you can have lunch (even do this before Jacques Torres) at Grimaldi's, which is a landmark, sitdown pizza place that was a favorite of Sinatra's. If you walk a block north first, on the way over, you can even stop by Gleason's gym, which has a storied history and has been the grungy digs for many past boxing champions.
Grimaldis sits right in the shadow of the Brooklyn Bridge. It's just a cool looking backdrop. It is also the only coal fired brick oven left that is allowed in NYC and it does something special to the pizza. They use only the freshest ingredients. It isn't typical looking or tasting pizza. Very thing crust, pools of the freshest mozzerella you have ever taste, instead of strings of it filling the whole slice, and whole basil leaves. It is sit down and you don't order by the slice. But it has a nice charm. Red checkered-clothed tables, Sinatra on the jukebox. Then about 200 yards ahead is the Fulton Ferry Landing where you get the most amazing view of Manhattan, again with the Bridge just off to your right and the Statue of Liberty to the left. There is an old lighthouse that has been converted into a large ice cream place there, and they make the ice cream on site. It is very creamy and rich. I'd recommending walking across the bridge if you wanted to do this little half day trip--it is a really cool walk--but it doesn't sound like Mrs. Moddy will be able to make it. If you do it by subway, it is the first subway stop out of Manhattan right off the A or the C trains. If you want to blow your wad on a nice dinner, right at the Fulton Ferry Landing is the River Cafe. It's one of the priciest restaurants in NY. The food is probably not quite worth what you blow to eat there, but you are paying for the ambience and the view--you see the skyline, the statue of liberty, etc.
If you are inclined to stay in Manhattan, and you like jazz, I'd recommend a trip to the Village Vanguard which is all the way down 7th Avenue in the village. Great history and still consistently gets the best players. But call ahead and make a reservation if you plan to go. I particularly know the Village well, because of where I've lived. If you want, PM me with any questions or for more suggestions, Moddy.