I think that this list really depends on how many small and independents you want to count.
The only major player is Bexley.
If you want to start splitting hairs, I can list plenty of penmakers that are independent, and manufacturing every part for their pens (excluding nibs of course.) If you want to count these, then you can get into.....
Michael's Fatboy Edison David Broadwell Bruno Corsini Joe Cali ...I could go on.
Dan Symonds Dan Furlano Bruce Boone Bruce Robbins Chris Manning Chris Thompson
I'm leaving people out, I know...
Don't forget Brian Goulet (Goulet Pen Company)! I'm another one of those 'small independents' everyone's talking about. But hey, how do you think these big companies became big? They all had to start somewhere!