Starbucks on Park/Naglee, or any Panera Bread. Also although can get crowded, there is a Starbuck with a special room to work in on Lawrence and El Camino.
But you know.. I've found nothing is better than a Library. Quieter and more conducive to working since everyone else is.
Mission City cafe, 2221 The Alameda. It's in Santa Clara, just outside S.J. Nice vibe, lots of students, open late.
The main library at 150 East San Fernando is awesome. Good coffee in the bottom, ample (private if you want) space in the eight floors. Open late cause it's shared with San Jose State.
But you know.. I've found nothing is better than a Library. Quieter and more conducive to working since everyone else is.