It's nearly a month since this asked this question, but here are some options:
Downtown, near the Village: Blicks has many sketchbooks, including Moleskine; nearby is New York Central and Utrechts; both have great supplies.
Downtown, near Church Street, Fountain Pen Hospital, has a huge selection of fountain pens.
Kate's Paper, also downtown, has lots of writing material and a fairly decent, but small selection of writing implements--pens.
Good luck and enjoy.