Rivendell carries very high end bikes, and from what I am told, they are easy to deal with. http://www.rivbike.com/
And then there is Harris Cyclery in West Newton, MA. These people know their bicycles. They employed the legendary Sheldon Brown before his death in 2008 , and the top people are still in charge there so you know that anybody working there is going to be a bicycle expert.http://sheldonbrown.com/harris/
There are plenty of other online shops that you can find with a quick internet search.
If this is your first bike, I need to stress how important it is that you visit your local bike shop(LBS). If you are in New York, you have a lot of them to choose from. Before you purchase your first bike, or the first in several years, you need to get fitted. A poorly fitting bicycle will be uncomfortable to ride. The biggest reason that people don't ride is because they are uncomfortable on their bikes. A fitting will get a bike the right size for you, and with a little tweaking and maybe a different stem, your bike will be comfortable to ride. A proper fitting takes 2 - 3 hours and might cost around $100, but it is time and money well spent. If you walk into a shop and they ask your inseam and then start showing you bikes, leave there and go to another shop.
It is also important that you test ride bikes when you are looking for your first one. Bikes made from different materials ride differently. Some manufacturers design and set up their bikes different than other manufacturers, and one might suit you better than another. The only way to be sure which is the right bike for you is to test ride them. As you become more familiar with the different bikes that are out there, you can look at a website and see which of their bikes would be best for you bu looking at the geometry and material of the frame.
Last but not least, it is good to have a good relationship with your LBS because you are going to need them someday. Rarely have I ever seen a LBS refuse to work on someone's internet purchased bike, I do know that they rarely do the special things, like put your repair order on top of the stack or do small repair for free, like they do for loyal customers who purchased their bike at that shop. Sometimes a shop will give special pricing to their loyal customers on accessories and clothing. One of our local shops has special sales and events, by invitation only, for their loyal customers. And I can't tell you how many times I have stopped by my LBS and had a set of bearings or cable ens handed to me at no charge because they now that I will be back when I need tires or a new chain. Being on good terms with your LBS can make your life a whole lot easier.