Either way, carry some chlorine tablets or iodine as a backup. Virtually no weight or bulk involved and if your steripen quits or your pump breaks, you still have a way to treat water quickly on the go instead of being forced to boil.
As far as filter vs. steripen, I think it depends a lot on where you are. If you're backpacking in an area with clean, flowing water, I'd probably go with the steripen. If you're forced to get sketchier water that's been standing, filter all the way.