I always see a bunch of people w/ laptops at the Bar at Cocoa bar: http://www.yelp.com/biz/cocoa-bar-new-york

Also there's usually a couple laptops out at Coyi Cafe up the streeet on Ave B.

Though I do agree that there's a shortage of good spots to hang out w/ a laptop for a few hours during the week daytime.

(not that this has any effect in my mind as to whether NY is better than SF for startups, but whatever)

I don't know to where OP is referring, but I've found Table 12 on Ave A & 12th to be a decent place to work. When I've gone during the day on weekdays it's usually half-empty, has free wifi, and the staff hasn't seemed to mind my loitering (though I do buy stuff).

Cafe Ghia, Jefferson stop of the L train. 24 Irving Avenue.

And their food is a lot better than Table 12 ;)