By far the best place to get (bare rooted) fruit trees in Ithaca is Cummins Nursery, owned by Steve Cummins, part of Indian Creek Farm on 1408 Trumansburg Road / rt 96N. You can call 607.227.6147 or email indiancreekfarm@yahoo.com for more information. They sell dwarf and full size apples, pears, stone fruits but also several raspberry & blackberry & blueberry varieties and great strawberries. We have planted fruit trees from several nurseries around town and only the Cummins Nursery plants thrived!
If you are looking for cheap bulk trees try the National Arbor Day Foundation. When you become a member they will gift you 10 trees, and they also have a Tree Store with very reasonable prices. Don't be surprised when you get the shipment, though, the little trees are like bare(ly) rooted sticks! But with a little TLC and fast planting they will grow fine.
If you are looking for specialty small fruiting plants, like elderberries, gooseberries and currants, Nourse Farms is a good option. Ask for their catalog and see what you like.
Turnbull Nursery Offer large quantities but don't give guaranties. Their stock is excellent quality and they are the cheapest suppliers on Currants and goosberries.
Oikos Tree Crops Offer a lot of varieties which are hard to get otherwise. Their potted seedlings are fine quality.
Of course, by far the best way to get plants you know will love this area is by dividing or rooting cutings from established plants. Ask around, place a craigslist ad, you'll never know what might come up. I bought rhubarb plants twice and could not get them through the winter; gave up on catalogs and placed a local ad, was offered to divide from a 50 year old patch of farm rhubarb and have not had any trouble since!
(Thank you, Angelika!)