I say NYC, IMO you can't go wrong with it. I haven't shopped for yarn in the city, but there should be plenty of stores. There's so much to do in the city that you could make it the whole vacation. Like Boston, you can get around without having a car. Maybe the subway isn't the cleanest place in the world, but it's cheap and gets you from point A to point B. Boston would be good for that too, but I'm a little biased because I live in Jersey.
If you are looking for a little more scenery artsy-ish, you can go to Ithaca, NY. It's really pretty when the leaves turn colors, but it kind of happens early. There are gorges that you can go to and many trails to walk on. Depending on the weather, you can swim (illegaly, but everyone does it) in the gorges. That's better in summertime into early Sept, but it's kind of been chilly. In the commons area there is a knitting store that sells a good array of yarn. Yea, I went to IC last year so that's why I mentioned it. I know in October they have Applefest which is held in the commons. A bunch of tables are set up and people sell apple related items (pie, cider, caramel apples, etc). If you were planning to go to NYC then Ithaca is about 3.5 hours, so I don't know if that's too much time or not.
I know the Berkshires in MA have plenty of trees that have pretty colors. It's very country-ish and I don't think it's too far from Boston. I used to have a country house in Otis which is in the Berkshires. There wasn't much around Otis and would have to travel to get to some kind of civilization.
I think your best bet is Boston or NYC. If you are going to travel by car to the destination I would probably say Boston because you have family there. At least you can park your car at their house and not have to pay for parking at the hotel.
On a kind of random note, Jersey is a nice place to visit. I don't think it's what you are looking for, but I have to defend it. We are not the armpit of America and all of Jersey doesn't smell like trash. Pretty sure if you go to any major city there are unpleasant smells all the time. You just have to know where to go and where not to go. Ok, I'm done with that rant that no one in this topic provoked.
I hope you enjoy your vacation wherever it may be. Actually, I know you will because who doesn't like a break from life?