I will be visiting family in NYC mid September to early October.

I have heard about how beautiful this area is during autumn and was hoping to spend a few days travelling north of the city (about 4-5 days) to enjoy this colourful time of the year. I appreciate that seasons do vary and like other seasons autumn can come early or late but all being well is there a "best time" to do this?

Also are there suggested routes to take that could include some coastline as well as rural and mountains - love exploring quaint towns.

Peak Fall foliage around NYC is actually quite a bit later than your time frame--maybe a month later, depending on the weather. I think you'd need to get as far as Vermont or the Adirondacks (4 hours or more of driving each way) for some some spectacular views, and even then you'd need to do it at the end of your trip. Many popular places peak around Columbus Day (Oct 12 or thereabouts),
You can still tour some really nice areas, like the Hudson Valley in NY, or Berkshires in Massachusetts--full of quaint towns ,but without much of the Autumn color change

You are too early. The Hudson valley has the best foliage in mid Oct. When you will be there the color is much further north. (Trees don;t change in the city until late Oct or early Nov.0

Sorry - Sept is till really summer in NY and you can expect warm temps - highs in the 80s are very common and it's sometimes really hot even until the end of Spet. Autumn in NY is really from mid oct on.

Actually, it's more like late October and maybe even November before the peak foliage hits the Hudson Valley. Still, even without the peak foliage, the area is beautiful and certainly still worth your time.
Tell us your interests and we'll pass along appropriate suggestions.