1. Hewes St. (J/Z) up 67.7%
While the area around Hewes is getting more built up, thus more passengers, the main reason for such a jump is because Marcy Ave's count went down because it was closed for construction part of the year. It's safe to say that many of those Marcy people walked to Hewes during that time.
2. Avenue X (F) up 56.1%
Ave X was the terminal for the F while stillwell was closed to the F.
4. Kosciusko St (J) up 25.9%
I think Kosciuzko St was closed for renovations for a period in 2002 (don't remember if that was 2001 though), but in addition, the area along the Broadway el has much new construction, thus more passengers. Chauncey St also went way up.
As for Bowery, the area above Bowery is being gentrified, many college aged people and young people are moving in, so the station will have steady increases in the coming years, it's days are also getting brighter.