Pneumatic floor nailer
I've used nearly all of them and it's hands down with this Bostich pneumatic Stapler. With the way it's built it brings boards together much tighter than the others without having to whack them with the rubber side of the mal. Furthermore a new one comes with felt padding under the plate that sits on top of the floor.
Good Luck with your project
You won't be able to use the staples for top or hand nailing as they'll bend on you. Furthermore a nail set doesn't work well with counter sinking staples if you fail to drive the staple in far enough when side nailing/stapling. In that case use a wide blade screwdriver turned sideways to countersink. I would suggest this tool or similiar for top and side nailing if you have alot of area to cover. Cost apprx $190
Not the greatest picture but it's a Porter Cable that can shoot 2 1/2" 16 guage nails.